Title: DBI/RJDBC interface to PostgreSQL Database
Diff between RpgSQL versions 0.1-5 dated 2011-05-12 and 0.1-6 dated 2012-12-22
Description: DBI interface to PostgreSQL database via RJDBC.
Author: G. Grothendieck
Maintainer: G. Grothendieck
DESCRIPTION | 8 ++++----
INSTALL | 39 +++++++++++++++++++++++++++++++--------
MD5 |only
NAMESPACE |only
NEWS | 6 ++++++
R/class.R | 4 ++--
6 files changed, 43 insertions(+), 14 deletions(-)
Title: Deprecated 'classic' Rcpp API
Diff between RcppClassic versions 0.9.2 dated 2012-07-24 and 0.9.3 dated 2012-12-22
Description: The RcppClassic package provides a deprecated C++ library
which facilitates the integration of R and C++. New projects
should use the new Rcpp API in the Rcpp package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
David Reiss, and based on code written during 2005 and 2006 by
Dominick Samperi
Maintainer: Dirk Eddelbuettel
ChangeLog | 13 ++++++
DESCRIPTION | 10 ++---
MD5 | 16 ++++----
inst/doc/RcppClassic-intro.pdf |binary
inst/doc/RcppClassic-unitTests.pdf |binary
inst/include/RcppClassic.h | 11 +++++
src/RcppResultSet.cpp | 32 +++++++++++++++--
vignettes/unitTests-results/RcppClassic-unitTests.html | 18 ++++-----
vignettes/unitTests-results/RcppClassic-unitTests.txt | 4 +-
9 files changed, 77 insertions(+), 27 deletions(-)
Title: Prototype object-based programming
Diff between proto versions 0.3-9.2 dated 2011-04-29 and 0.3-10 dated 2012-12-22
Description: An object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.
Author: Louis Kates, Thomas Petzoldt
Maintainer: Gabor Grothendieck
proto-0.3-10/proto/DESCRIPTION | 8 ++++----
proto-0.3-10/proto/MD5 |only
proto-0.3-10/proto/NAMESPACE |only
proto-0.3-10/proto/inst/NEWS | 6 ++++++
proto-0.3-10/proto/inst/doc/proto.pdf |binary
proto-0.3-10/proto/inst/doc/protoref.pdf |binary
proto-0.3-10/proto/vignettes |only
proto-0.3-9.2/proto/inst/doc/README |only
proto-0.3-9.2/proto/inst/doc/Z.cls |only
proto-0.3-9.2/proto/inst/doc/cloning3.dot |only
proto-0.3-9.2/proto/inst/doc/cloning3.pdf |only
proto-0.3-9.2/proto/inst/doc/jss.bst |only
proto-0.3-9.2/proto/inst/doc/proto-dot.pdf |only
proto-0.3-9.2/proto/inst/doc/proto-dot.tex |only
proto-0.3-9.2/proto/inst/doc/proto-raw |only
proto-0.3-9.2/proto/inst/doc/proto-raw.tex |only
proto-0.3-9.2/proto/inst/doc/proto-smoothing03.pdf |only
proto-0.3-9.2/proto/inst/doc/proto-smoothing03.tex |only
proto-0.3-9.2/proto/inst/doc/proto-smoothing04.pdf |only
proto-0.3-9.2/proto/inst/doc/proto-smoothing04.tex |only
proto-0.3-9.2/proto/inst/doc/proto-smoothing06.pdf |only
proto-0.3-9.2/proto/inst/doc/proto-smoothing06.tex |only
proto-0.3-9.2/proto/inst/doc/proto-smoothing10.pdf |only
proto-0.3-9.2/proto/inst/doc/proto-smoothing10.tex |only
proto-0.3-9.2/proto/inst/doc/proto.bib |only
proto-0.3-9.2/proto/inst/doc/proto.tex |only
proto-0.3-9.2/proto/inst/doc/protoref-raw.tex |only
27 files changed, 10 insertions(+), 4 deletions(-)
Title: Non-linear regression with brute force
Diff between nls2 versions 0.1-3 dated 2010-08-23 and 0.1-4 dated 2012-12-22
Description: Adds algorithm="brute-force" and multiple starting values
to nls.
Author: G. Grothendieck
Maintainer: G. Grothendieck
nls2-0.1-3/nls2/R/as.lm.R |only
nls2-0.1-3/nls2/man/as.lm.nls.Rd |only
nls2-0.1-4/nls2/DESCRIPTION | 8 ++++----
nls2-0.1-4/nls2/MD5 |only
nls2-0.1-4/nls2/NAMESPACE |only
nls2-0.1-4/nls2/NEWS | 6 ++++++
nls2-0.1-4/nls2/R/nls2.R | 13 ++++++++++---
nls2-0.1-4/nls2/man/nls2.Rd | 3 ++-
8 files changed, 22 insertions(+), 8 deletions(-)
Title: Time Series Regression
Diff between dyn versions 0.2-8.1 dated 2012-03-24 and 0.2-9 dated 2012-12-22
Description: Time series regression. The dyn class interfaces ts,
irts, its, zoo and zooreg time series classes to lm, glm,
loess, quantreg::rq, MASS::rlm, MCMCpack::MCMCregress,
quantreg::rq, randomForest::randomForest and other regression
functions allowing those functions to be used with time series
including specifications that may contain lags, diffs and
missing values.
Author: G. Grothendieck
Maintainer: G. Grothendieck
dyn-0.2-8.1/dyn/inst/NEWS |only
dyn-0.2-9/dyn/DESCRIPTION | 8 ++++----
dyn-0.2-9/dyn/MD5 | 8 ++++----
dyn-0.2-9/dyn/NAMESPACE | 11 +----------
dyn-0.2-9/dyn/NEWS |only
dyn-0.2-9/dyn/data/baltimore.rda |binary
6 files changed, 9 insertions(+), 18 deletions(-)
Title: Rigorous - NIfTI+ANALYZE+AFNI Input / Output
Diff between oro.nifti versions 0.3.5 dated 2012-09-16 and 0.3.8 dated 2012-12-22
Description: Functions for the input/output and visualization of
medical imaging data that follow either the ANALYZE, NIfTI or
AFNI formats. This package is part of the Rigorous Analytics
bundle.
Author: Brandon Whitcher, Volker Schmid and Andrew Thornton, with
contributions by Karsten Tabelow and Jon Clayden
Maintainer: Brandon Whitcher
DESCRIPTION | 16 +-
MD5 | 78 +++++-----
R/auditTrail.R | 39 +----
R/convert_nifti.R | 39 +----
R/niftiS4.R | 9 +
R/readS4.R | 65 +++++---
R/zzz.R | 7
inst/doc/nifti.Rnw | 66 +++++---
inst/doc/nifti.pdf |binary
man/anlz-class.Rd | 2
man/anlz.Rd | 2
man/as_nifti.Rd | 2
man/audit_trail.Rd | 29 ++-
man/aux_file-methods.Rd | 4
man/bitwise.Rd | 2
man/calmin-methods.Rd | 2
man/coerce-methods.Rd | 2
man/convert_anlz.Rd | 2
man/convert_nifti.Rd | 2
man/descrip-methods.Rd | 2
man/image-methods.Rd | 2
man/miscellaneous.Rd | 2
man/nifti-class.Rd | 2
man/nifti.Rd | 4
man/niftiExtensionSection-class.Rd | 2
man/oro2fmri.Rd | 2
man/orthographic-methods.Rd | 2
man/overlay-methods.Rd | 2
man/pixdim-methods.Rd | 2
man/q2R.Rd | 2
man/qformsform.Rd | 2
man/read_anlz.Rd | 20 --
man/read_nifti.Rd | 13 +
man/remove.Rd | 2
man/reorient.Rd | 2
man/write_anlz.Rd | 2
man/write_nifti.Rd | 2
tests/Examples/oro.nifti-Ex.Rout.save | 252 +++++++++-------------------------
vignettes/nifti.Rnw | 66 +++++---
vignettes/nifti.bib | 24 +--
40 files changed, 344 insertions(+), 433 deletions(-)
Title: Estimation, simulation and visualization of Hierarchical
Archimedean Copulae (HAC)
Diff between HAC versions 0.2-5 dated 2012-10-11 and 0.2-6 dated 2012-12-22
Description: Package provides the estimation of the structure and the
parameters, simulation methods and structural plots of
high-dimensional Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin
Maintainer: Alexander Ristig
HAC-0.2-5/HAC/R/copula_aggregate.r |only
HAC-0.2-5/HAC/R/copula_cdf.r |only
HAC-0.2-5/HAC/R/copula_constructor.r |only
HAC-0.2-5/HAC/R/copula_empirical.r |only
HAC-0.2-5/HAC/R/copula_estimate.r |only
HAC-0.2-5/HAC/R/copula_functions.r |only
HAC-0.2-5/HAC/R/copula_pdf.r |only
HAC-0.2-5/HAC/R/copula_plot.r |only
HAC-0.2-5/HAC/R/copula_simulate.r |only
HAC-0.2-6/HAC/ChangeLog | 4 ++++
HAC-0.2-6/HAC/DESCRIPTION | 10 +++++-----
HAC-0.2-6/HAC/MD5 | 24 ++++++++++++------------
HAC-0.2-6/HAC/R/aggregate.r |only
HAC-0.2-6/HAC/R/cdf.r |only
HAC-0.2-6/HAC/R/constructor.r |only
HAC-0.2-6/HAC/R/empirical.r |only
HAC-0.2-6/HAC/R/estimate.r |only
HAC-0.2-6/HAC/R/functions.r |only
HAC-0.2-6/HAC/R/pdf.r |only
HAC-0.2-6/HAC/R/plot.r |only
HAC-0.2-6/HAC/R/simulate.r |only
HAC-0.2-6/HAC/man/estimate.copula.Rd | 2 +-
22 files changed, 22 insertions(+), 18 deletions(-)
Title: distances and routes on geographical grids
Diff between gdistance versions 1.1-3 dated 2012-05-25 and 1.1-4 dated 2012-12-22
Description: Calculate distances and routes on geographic grids.
Author: Jacob van Etten
Maintainer: Jacob van Etten
ChangeLog | 7 +++++++
DESCRIPTION | 13 +++++++------
MD5 | 38 +++++++++++++++++++-------------------
NAMESPACE | 2 +-
R/AAATransition-class.R | 8 ++------
R/Transition-extract-replace.R | 2 +-
R/accCost.R | 2 +-
R/adjacency.R | 16 ++++++++--------
R/coerce.R | 7 +------
R/costDistance.R | 21 ++++++---------------
R/internal-functions.R | 4 ----
R/shortestPath.R | 19 ++++++++++---------
R/transition.R | 18 +++++++++---------
data/genDist.RData |binary
data/popCoord.RData |binary
inst/doc/gdistance-vignette.Rnw | 11 +++++------
inst/doc/gdistance-vignette.pdf |binary
man/accCost.Rd | 2 +-
man/adjacency.Rd | 2 +-
man/transition.Rd | 4 ++--
20 files changed, 81 insertions(+), 95 deletions(-)
Title: HIBAG -- HLA Genotype Imputation with Attribute Bagging
Diff between HIBAG versions 0.9.3 dated 2012-10-20 and 0.9.4 dated 2012-12-22
Description: To impute HLA types from unphased SNP data using an
attribute bagging method.
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 8 -
MD5 | 18 +--
NEWS | 6 +
R/main.r | 70 +++-----------
man/HIBAG-package.Rd | 4
man/hlaAllele.Rd | 4
man/hlaBED2Geno.Rd | 2
src/LibHLA.cpp | 139 +++++-----------------------
src/LibHLA.h | 250 ++++++++++++++++++++++++++++++++++++++-------------
src/main.cpp | 6 -
10 files changed, 263 insertions(+), 244 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-02-28 0.1-2
2007-11-17 0.1-1
2007-11-08 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-24 1.1
2012-03-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-10-11 1.0
2011-07-06 0.1.2
2011-04-11 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-02-25 1.0.2-1
2007-04-16 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-12-04 1.0-7
2008-01-27 1.0-6
2007-10-15 1.0-5
2005-12-11 1.0-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-01-15 1.0-3
2007-04-12 1.0-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-04-10 1.1-4
2008-02-22 1.1-3
2007-11-11 1.1-2
2007-11-09 1.1-1
2007-11-08 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-11-08 0.1-5
2009-05-19 0.1-4
2008-02-28 0.1-3
2007-12-24 0.1-2
2006-09-29 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2003-12-10 1.2-14
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-05-11 1.2
2010-11-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-02-29 0.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-01-23 0.6-3
2005-02-25 0.6-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-01-24 0.9-9
2010-01-23 0.9-8
2010-01-22 0.9-7
2010-01-21 0.9-6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-11-25 1.0
Title: Everyone's Statistical Software
Diff between Zelig versions 4.1-0 dated 2012-11-13 and 4.1-1 dated 2012-12-22
Description: Zelig is an easy-to-use program that can estimate, and
help interpret the results of, an enormous range of statistical
models. It literally is ``everyone's statistical software''
because Zelig's simple unified framework incorporates everyone
else's (R) code. We also hope it will become ``everyone's
statistical software'' for applications and teaching, and so
have designed Zelig so that anyone can easily use it or add
their programs to it. Zelig also comes with infrastructure
that facilitates the use of any existing method, such as by
allowing multiply imputed data for any model, and mimicking the
program Clarify (for Stata) that takes the raw output of
existing statistical procedures and translates them into
quantities of direct interest.
Author: Matt Owen
Maintainer: Matt Owen
Zelig-4.1-0/Zelig/man/summary.Relogit.Rd |only
Zelig-4.1-0/Zelig/tests/bootstrap.R |only
Zelig-4.1-0/Zelig/xxxx |only
Zelig-4.1-1/Zelig/DESCRIPTION | 6 -
Zelig-4.1-1/Zelig/MD5 | 95 +++++++++++----------------
Zelig-4.1-1/Zelig/NAMESPACE | 3
Zelig-4.1-1/Zelig/R/Zelig-package.R | 2
Zelig-4.1-1/Zelig/R/exp.R | 19 +++--
Zelig-4.1-1/Zelig/R/gamma.R | 8 +-
Zelig-4.1-1/Zelig/R/gamma.survey.R | 15 ++--
Zelig-4.1-1/Zelig/R/logit.R | 9 +-
Zelig-4.1-1/Zelig/R/logit.survey.R | 15 +---
Zelig-4.1-1/Zelig/R/ls.R | 9 +-
Zelig-4.1-1/Zelig/R/negbinom.R | 10 +-
Zelig-4.1-1/Zelig/R/normal.R | 8 +-
Zelig-4.1-1/Zelig/R/normal.survey.R | 11 +--
Zelig-4.1-1/Zelig/R/plots.R | 96 +++++++++++++++++++++++-----
Zelig-4.1-1/Zelig/R/poisson.R | 10 +-
Zelig-4.1-1/Zelig/R/poisson.survey.R | 14 +---
Zelig-4.1-1/Zelig/R/print.R | 44 +++++++++++-
Zelig-4.1-1/Zelig/R/probit.survey.R | 14 +---
Zelig-4.1-1/Zelig/R/relogit.R | 20 ++++-
Zelig-4.1-1/Zelig/R/setx.R | 14 +++-
Zelig-4.1-1/Zelig/R/sim.default.R | 29 ++++++++
Zelig-4.1-1/Zelig/R/summary.R | 27 +++++++
Zelig-4.1-1/Zelig/R/tobit.R | 21 ++++--
Zelig-4.1-1/Zelig/R/zelig.R | 12 ++-
Zelig-4.1-1/Zelig/R/zzz.R | 12 +--
Zelig-4.1-1/Zelig/demo/00Index | 1
Zelig-4.1-1/Zelig/demo/relogit.R |only
Zelig-4.1-1/Zelig/inst/doc/gamma.pdf |binary
Zelig-4.1-1/Zelig/inst/doc/logit.pdf |binary
Zelig-4.1-1/Zelig/inst/doc/ls.pdf |binary
Zelig-4.1-1/Zelig/inst/doc/manual-bayes.pdf |binary
Zelig-4.1-1/Zelig/inst/doc/manual-gee.pdf |binary
Zelig-4.1-1/Zelig/inst/doc/manual.pdf |binary
Zelig-4.1-1/Zelig/inst/doc/normal.pdf |binary
Zelig-4.1-1/Zelig/inst/doc/twosls.pdf |binary
Zelig-4.1-1/Zelig/man/summary.relogit.Rd |only
Zelig-4.1-1/Zelig/tests/mix.R |only
Zelig-4.1-1/Zelig/tests/models-core.R | 17 ++++
Zelig-4.1-1/Zelig/tests/models-survey.R | 3
Zelig-4.1-1/Zelig/tests/plot-ci.R | 16 ++++
43 files changed, 384 insertions(+), 176 deletions(-)
Title: Various programming utilities
Diff between R.utils versions 1.18.0 dated 2012-11-01 and 1.19.3 dated 2012-12-22
Description: This package provides utility methods useful when
programming and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
R.utils-1.18.0/R.utils/R/Sys.setenv.patch.R |only
R.utils-1.18.0/R.utils/R/as.character.hexmode,patch.R |only
R.utils-1.18.0/R.utils/man/Sys.setenv.Rd |only
R.utils-1.18.0/R.utils/man/lapply.MultiVerbose.Rd |only
R.utils-1.19.3/R.utils/DESCRIPTION | 18
R.utils-1.19.3/R.utils/MD5 | 49 +-
R.utils-1.19.3/R.utils/NAMESPACE | 361 +++++++++++++++++-
R.utils-1.19.3/R.utils/R/006.fixVarArgs.R | 7
R.utils-1.19.3/R.utils/R/999.NonDocumentedObjects.R | 2
R.utils-1.19.3/R.utils/R/Arguments.R | 41 +-
R.utils-1.19.3/R.utils/R/MultiVerbose.R | 25 -
R.utils-1.19.3/R.utils/R/Verbose.R | 2
R.utils-1.19.3/R.utils/R/addFinalizerToLast.R | 6
R.utils-1.19.3/R.utils/R/bunzip2.R | 6
R.utils-1.19.3/R.utils/R/countLines.R | 6
R.utils-1.19.3/R.utils/R/createLink.R | 16
R.utils-1.19.3/R.utils/R/gzip.R | 9
R.utils-1.19.3/R.utils/R/moveInSearchPath.R | 5
R.utils-1.19.3/R.utils/R/pushBackupFile.R | 2
R.utils-1.19.3/R.utils/R/queryRCmdCheck.R | 8
R.utils-1.19.3/R.utils/R/writeDataFrame.R | 17
R.utils-1.19.3/R.utils/R/zzz.R | 77 +--
R.utils-1.19.3/R.utils/inst/NEWS | 48 ++
R.utils-1.19.3/R.utils/man/MultiVerbose.Rd | 2
R.utils-1.19.3/R.utils/man/as.list.MultiVerbose.Rd |only
R.utils-1.19.3/R.utils/man/createLink.Rd | 14
R.utils-1.19.3/R.utils/man/writeRaw.MultiVerbose.Rd | 5
R.utils-1.19.3/R.utils/tests/queryRCmdCheck.R | 2
28 files changed, 587 insertions(+), 141 deletions(-)
Title: Easy handling of and access to files organized in structured
directories
Diff between R.filesets versions 1.6.0 dated 2012-11-15 and 1.9.0 dated 2012-12-22
Description: A file set refers to a set of files located in one or more
directories on the file system. This package provides classes
and methods to locate, setup, subset, navigate and iterate such
sets. The API is designed such that these classes can be
extended via inheritance to provide a richer API for special
file formats. Moreover, a specific name format is defined such
that filenames and directories can be considered to have
fullnames which consists of a name followed by comma-separated
tags. This adds additional flexibility to identify file sets
and individual files. NOTE: This package's API should be
considered to be in an beta stage. Its main purpose is
currently to support the aroma.* packages, where it is one of
the main core components; if you decide to build on top of this
package, please contact the author first.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
R.filesets-1.6.0/R.filesets/man/lapply.GenericDataFileSet.Rd |only
R.filesets-1.6.0/R.filesets/man/writeColumnsToFiles.TabularTextFile.Rd |only
R.filesets-1.9.0/R.filesets/DESCRIPTION | 20
R.filesets-1.9.0/R.filesets/MD5 | 68 +-
R.filesets-1.9.0/R.filesets/NAMESPACE | 210 ++++++
R.filesets-1.9.0/R.filesets/R/999.DEPRECATED.R | 35 +
R.filesets-1.9.0/R.filesets/R/FullNameInterface.R | 6
R.filesets-1.9.0/R.filesets/R/GenericDataFile.R | 88 +-
R.filesets-1.9.0/R.filesets/R/GenericDataFileSet.R | 334 +++++-----
R.filesets-1.9.0/R.filesets/R/GenericDataFileSetList.R | 45 -
R.filesets-1.9.0/R.filesets/R/GenericTabularFile.R | 63 +
R.filesets-1.9.0/R.filesets/R/GenericTabularFile.writeColumnsToFiles.R | 13
R.filesets-1.9.0/R.filesets/R/TabularTextFile.R | 116 ++-
R.filesets-1.9.0/R.filesets/R/TabularTextFileSet.R | 27
R.filesets-1.9.0/R.filesets/R/zzz.R | 4
R.filesets-1.9.0/R.filesets/incl/999.missingdocs.txt | 12
R.filesets-1.9.0/R.filesets/incl/TabularTextFileSet.readDataFrame.Rex | 8
R.filesets-1.9.0/R.filesets/inst/NEWS | 79 ++
R.filesets-1.9.0/R.filesets/man/FullNameInterface.Rd | 1
R.filesets-1.9.0/R.filesets/man/GenericDataFile.Rd | 3
R.filesets-1.9.0/R.filesets/man/GenericDataFileSet.Rd | 6
R.filesets-1.9.0/R.filesets/man/GenericDataFileSetList.Rd | 6
R.filesets-1.9.0/R.filesets/man/GenericTabularFile.Rd | 12
R.filesets-1.9.0/R.filesets/man/GenericTabularFileSet.Rd | 4
R.filesets-1.9.0/R.filesets/man/Non-documented_objects.Rd | 12
R.filesets-1.9.0/R.filesets/man/TabularTextFile.Rd | 11
R.filesets-1.9.0/R.filesets/man/TabularTextFileSet.Rd | 4
R.filesets-1.9.0/R.filesets/man/as.list.GenericDataFileSet.Rd | 5
R.filesets-1.9.0/R.filesets/man/getDefaultColumnNames.TabularTextFile.Rd | 2
R.filesets-1.9.0/R.filesets/man/getFilename.GenericDataFile.Rd | 2
R.filesets-1.9.0/R.filesets/man/getPath.GenericDataFile.Rd | 2
R.filesets-1.9.0/R.filesets/man/getPathname.GenericDataFile.Rd | 7
R.filesets-1.9.0/R.filesets/man/gzip.GenericDataFile.Rd | 8
R.filesets-1.9.0/R.filesets/man/readColumns.GenericTabularFile.Rd |only
R.filesets-1.9.0/R.filesets/man/readDataFrame.GenericTabularFile.Rd | 4
R.filesets-1.9.0/R.filesets/man/readDataFrame.TabularTextFileSet.Rd | 10
R.filesets-1.9.0/R.filesets/man/writeColumnsToFiles.GenericTabularFile.Rd |only
37 files changed, 879 insertions(+), 348 deletions(-)
Title: Core methods and classes used by aroma.* packages part of The
Aroma Framework
Diff between aroma.core versions 2.7.0 dated 2012-11-25 and 2.8.0 dated 2012-12-22
Description: This package contains core methods and classes used by
higher-level aroma.* packages part of the Aroma Project, e.g.
aroma.affymetrix and aroma.cn. Its API should be considered to
be in alpha and beta versions, and is mostly of interest to
developers.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
aroma.core-2.7.0/aroma.core/inst/archive |only
aroma.core-2.7.0/aroma.core/inst/reports/templates/html/archive |only
aroma.core-2.7.0/aroma.core/inst/reports/templates/rsp/archive |only
aroma.core-2.8.0/aroma.core/DESCRIPTION | 18
aroma.core-2.8.0/aroma.core/MD5 | 228 +++-------
aroma.core-2.8.0/aroma.core/R/AromaCellSequenceFile.R | 5
aroma.core-2.8.0/aroma.core/R/AromaCellSequenceFile.REPEATS.R | 4
aroma.core-2.8.0/aroma.core/R/AromaCellSequenceFile.SNPs.R | 4
aroma.core-2.8.0/aroma.core/R/AromaGenomeTextFile.R | 7
aroma.core-2.8.0/aroma.core/R/AromaMicroarrayDataFile.R | 4
aroma.core-2.8.0/aroma.core/R/AromaMicroarrayDataSet.R | 10
aroma.core-2.8.0/aroma.core/R/AromaMicroarrayDataSetTuple.R | 2
aroma.core-2.8.0/aroma.core/R/AromaSettings.R | 7
aroma.core-2.8.0/aroma.core/R/AromaTabularBinaryFile.R | 14
aroma.core-2.8.0/aroma.core/R/AromaTransform.R | 4
aroma.core-2.8.0/aroma.core/R/AromaUcscGenomeTextFile.R | 4
aroma.core-2.8.0/aroma.core/R/AromaUflFile.R | 4
aroma.core-2.8.0/aroma.core/R/AromaUgpFile.R | 4
aroma.core-2.8.0/aroma.core/R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R | 8
aroma.core-2.8.0/aroma.core/R/AromaUnitPscnBinarySet.R | 9
aroma.core-2.8.0/aroma.core/R/AromaUnitSignalBinarySet.R | 6
aroma.core-2.8.0/aroma.core/R/AromaUnitSignalBinarySet.writeDataFrame.R | 2
aroma.core-2.8.0/aroma.core/R/AromaUnitTotalCnBinaryFileList.R | 2
aroma.core-2.8.0/aroma.core/R/AromaUnitTotalCnBinarySet.R | 11
aroma.core-2.8.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 13
aroma.core-2.8.0/aroma.core/R/AromaUnitTotalCnBinarySetTuple.R | 3
aroma.core-2.8.0/aroma.core/R/CacheKeyInterface.R |only
aroma.core-2.8.0/aroma.core/R/ChromosomalModel.R | 6
aroma.core-2.8.0/aroma.core/R/ChromosomalModel.drawCytoband.R | 4
aroma.core-2.8.0/aroma.core/R/CopyNumberDataSetTuple.R | 10
aroma.core-2.8.0/aroma.core/R/FileCacheKeyInterface.R |only
aroma.core-2.8.0/aroma.core/R/GenericTabularFileSet.calculateAverageColumnAcrossFiles.R | 12
aroma.core-2.8.0/aroma.core/R/GladModel.onFitAddGenotypeCalls.R | 6
aroma.core-2.8.0/aroma.core/R/RasterImage.R | 6
aroma.core-2.8.0/aroma.core/R/SampleAnnotationFile.R | 3
aroma.core-2.8.0/aroma.core/R/SegmentationDataFile.R | 3
aroma.core-2.8.0/aroma.core/R/TextUnitNamesFile.R | 3
aroma.core-2.8.0/aroma.core/R/profileCGH.plotRawCNs.R | 3
aroma.core-2.8.0/aroma.core/R/zzz.R | 5
aroma.core-2.8.0/aroma.core/incl/999.missingdocs.txt | 6
aroma.core-2.8.0/aroma.core/inst/NEWS | 39 +
aroma.core-2.8.0/aroma.core/man/AromaCellTabularBinaryFile.Rd | 26 -
aroma.core-2.8.0/aroma.core/man/AromaGenomeTextFile.Rd | 22
aroma.core-2.8.0/aroma.core/man/AromaMicroarrayDataFile.Rd | 18
aroma.core-2.8.0/aroma.core/man/AromaMicroarrayDataSet.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaMicroarrayDataSetTuple.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd | 24 -
aroma.core-2.8.0/aroma.core/man/AromaPlatform.Rd | 2
aroma.core-2.8.0/aroma.core/man/AromaRepository.Rd | 2
aroma.core-2.8.0/aroma.core/man/AromaTabularBinaryFile.Rd | 21
aroma.core-2.8.0/aroma.core/man/AromaTabularBinarySet.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaTransform.Rd | 2
aroma.core-2.8.0/aroma.core/man/AromaUnitCallFile.Rd | 26 -
aroma.core-2.8.0/aroma.core/man/AromaUnitCallSet.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaUnitFracBCnBinaryFile.Rd | 26 -
aroma.core-2.8.0/aroma.core/man/AromaUnitFracBCnBinarySet.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaUnitGenotypeCallFile.Rd | 28 -
aroma.core-2.8.0/aroma.core/man/AromaUnitGenotypeCallSet.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaUnitPscnBinaryFile.Rd | 28 -
aroma.core-2.8.0/aroma.core/man/AromaUnitPscnBinarySet.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaUnitSignalBinaryFile.Rd | 24 -
aroma.core-2.8.0/aroma.core/man/AromaUnitSignalBinarySet.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaUnitTabularBinaryFile.Rd | 28 -
aroma.core-2.8.0/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd | 28 -
aroma.core-2.8.0/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 4
aroma.core-2.8.0/aroma.core/man/AromaUnitTypesFile.Rd | 30 -
aroma.core-2.8.0/aroma.core/man/CacheKeyInterface.Rd |only
aroma.core-2.8.0/aroma.core/man/CbsModel.Rd | 2
aroma.core-2.8.0/aroma.core/man/ChromosomalModel.Rd | 2
aroma.core-2.8.0/aroma.core/man/ChromosomeExplorer.Rd | 2
aroma.core-2.8.0/aroma.core/man/CopyNumberChromosomalModel.Rd | 2
aroma.core-2.8.0/aroma.core/man/CopyNumberSegmentationModel.Rd | 2
aroma.core-2.8.0/aroma.core/man/Explorer.Rd | 2
aroma.core-2.8.0/aroma.core/man/FileCacheKeyInterface.Rd |only
aroma.core-2.8.0/aroma.core/man/GladModel.Rd | 2
aroma.core-2.8.0/aroma.core/man/HaarSegModel.Rd | 2
aroma.core-2.8.0/aroma.core/man/Non-documented_objects.Rd | 5
aroma.core-2.8.0/aroma.core/man/NonPairedPSCNData.Rd | 7
aroma.core-2.8.0/aroma.core/man/PairedPSCNData.Rd | 6
aroma.core-2.8.0/aroma.core/man/RawAlleleBFractions.Rd | 4
aroma.core-2.8.0/aroma.core/man/RawCopyNumberModel.Rd | 2
aroma.core-2.8.0/aroma.core/man/RawCopyNumbers.Rd | 4
aroma.core-2.8.0/aroma.core/man/RawGenomicSignals.Rd | 3
aroma.core-2.8.0/aroma.core/man/RawMirroredAlleleBFractions.Rd | 4
aroma.core-2.8.0/aroma.core/man/RawSequenceReads.Rd | 4
aroma.core-2.8.0/aroma.core/man/SegmentedAlleleBFractions.Rd | 4
aroma.core-2.8.0/aroma.core/man/SegmentedCopyNumbers.Rd | 4
aroma.core-2.8.0/aroma.core/man/getCacheKey.CacheKeyInterface.Rd |only
aroma.core-2.8.0/aroma.core/man/getCacheKey.FileCacheKeyInterface.Rd |only
89 files changed, 533 insertions(+), 380 deletions(-)
Title: Analysis of large Affymetrix microarray data sets
Diff between aroma.affymetrix versions 2.7.0 dated 2012-11-26 and 2.8.0 dated 2012-12-22
More information about aroma.affymetrix at CRAN
Description: This package implements classes for files and sets of
files for various Affymetrix file formats, e.g.
AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
These are designed to be memory efficient but still being fast.
The idea is to keep all data on file and only read data into
memory when needed. Clever caching mechanisms are used to
minimize the overhead of data IO. All of the above is hidden
in the package API and for the developer (and the end user),
the data is queried as if it lives in memory. With this design
it is only the diskspace that limits the number of arrays that
can be analyzed. To install, do:
source("http://www.aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix").
Author: Henrik Bengtsson, James Bullard, Kasper Hansen, Pierre Neuvial,
Elizabeth Purdom, Mark Robinson, Ken Simpson
Maintainer: Henrik Bengtsson
aroma.affymetrix-2.7.0/aroma.affymetrix/R/findCdf2.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,default,UGP+UFL,na26.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,default,UGP+UFL,na26.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,default,UGP+UFL,na27.1.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/test20120825,GSE12702,TCNs,crossplatform.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/test20070823,500K,TumorNormal,CN.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/test20090116,250K,TumorNormal,ASCN.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/test20090117,250K,TumorNormal,ASCN,pairy.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Mapping250K_Nsp.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Mapping250K_Sty.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Mapping250K_Nsp.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Mapping250K_Sty.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Mapping250K_Nsp.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Mapping250K_Sty.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Mapping250K_Nsp.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Mapping250K_Sty.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01a.downloadAnnotationData.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/01a.downloadAnnotationData.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01a.downloadAnnotationData.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/11.GcRmaBackgroundCorrection.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,GcContentNormalization.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1,SmoothNormalization.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,ChromosomeExplorer.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01a.downloadAnnotationData.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20070412,100K,CN.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20070412,100K.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20070922,100K,CN,paired.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20071006,100K,CN,hetero.Rhide |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080311,100K,CN,QA.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080428,100K,CN,allele.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080623,100K,BCN.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080721,100K,BPN.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080730,100K,BPN,alleleSpecific.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080830,100K,ACC,mergeShifts.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20100210,100K,CN,XYbias.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20100525,100K,doCBS,tuple.R |only
aroma.affymetrix-2.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20100526,100K,tuple,fnt.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/DESCRIPTION | 18
aroma.affymetrix-2.8.0/aroma.affymetrix/MD5 | 519 +++++-----
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AbstractProbeSequenceNormalization.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffyGenePDInfo.writeCdf.R | 304 ++++-
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixAptSummaryFile.R | 12
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.COUNTS.R | 9
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.MONOCELL.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 44
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.UNIQUE.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.computeAffinities.R | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleCellPairs.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs3.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.getCellQuartets.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.getProbeSequenceData.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfCellIndices.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupCellMap.R | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R | 18
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCdfFile.readDataFrame.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCelFile.R | 15
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCelSet.R | 31
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R | 38
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCelSet.getAverageFile.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCnChpFile.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 7
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.R | 12
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.XTRS.R | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixProbeTabFile.R | 13
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AffymetrixTabularFile.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AromaCellSequenceFile.AFFX.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AromaChipTypeAnnotationFile.R | 22
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AromaUfcFile.R | 13
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AromaUflFile.AFFX.R | 7
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AromaUgpFile.AFFX.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/AromaUnitGcContentFile.AFFX.R | 7
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ChipEffectFile.R | 45
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ChipEffectSet.R | 27
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ChipEffectSet.getBaseline.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ChipEffectSet.xam.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ChromosomalModel.AFFX.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/CnChipEffectFile.R | 104 +-
aroma.affymetrix-2.8.0/aroma.affymetrix/R/CnChipEffectSet.R | 14
aroma.affymetrix-2.8.0/aroma.affymetrix/R/CnProbeAffinityFile.R | 65 +
aroma.affymetrix-2.8.0/aroma.affymetrix/R/CnagCfhSet.R | 16
aroma.affymetrix-2.8.0/aroma.affymetrix/R/CrlmmModel.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/DChipDcpSet.extras.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ExonChipEffectFile.R | 75 +
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ExonChipEffectSet.R | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ExonProbeAffinityFile.R | 58 +
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ExonRmaPlm.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ExonRmaPlm.calculateWeights.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/FirmaFile.R | 43
aroma.affymetrix-2.8.0/aroma.affymetrix/R/FirmaSet.R | 31
aroma.affymetrix-2.8.0/aroma.affymetrix/R/GcContentNormalization.R | 5
aroma.affymetrix-2.8.0/aroma.affymetrix/R/GenomeInformation.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/MatNormalization.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/MatSmoothing.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ParameterCelFile.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ProbeAffinityFile.R | 34
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ProbeLevelModel.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ProbeLevelModel.calculateWeights.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ProbeLevelModel.fit.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ProbeLevelTransform3.R | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/R/QualityAssessmentModel.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/QuantileNormalization.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ResidualFile.R | 40
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ResidualSet.R | 37
aroma.affymetrix-2.8.0/aroma.affymetrix/R/ScaleNormalization.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/SnpChipEffectFile.R | 115 +-
aroma.affymetrix-2.8.0/aroma.affymetrix/R/SnpChipEffectNnn.extractCNT.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/SnpChipEffectSet.R | 24
aroma.affymetrix-2.8.0/aroma.affymetrix/R/SnpInformation.R | 3
aroma.affymetrix-2.8.0/aroma.affymetrix/R/SnpProbeAffinityFile.R | 57 +
aroma.affymetrix-2.8.0/aroma.affymetrix/R/SpatialReporter.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/R/WeightsFile.R | 44
aroma.affymetrix-2.8.0/aroma.affymetrix/R/WeightsSet.R | 29
aroma.affymetrix-2.8.0/aroma.affymetrix/R/createExonByTranscriptCdf.R | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/R/findByCdf2.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/R/zzz.R | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/incl/999.missingdocs.txt | 20
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/NEWS | 85 +
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GWS5,default,UGP+UFL,na26.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GWS6,default,UGP+UFL,na26.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GWS6,default,UGP+UFL,na27.1.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27/GenomeWideSNP_6,UGC,na27.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na28/Mapping250K_Nsp,UGC,na28.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na28/Mapping250K_Sty,UGC,na28.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACP.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,UGP.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/R/downloadUtils.R | 48
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/11.doASCRMAv2,TCNs,500K.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/annotation |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/21.TCN,500K.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN,paired.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Nsp.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Sty.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Nsp.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Sty.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Nsp.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Sty.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Nsp.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Sty.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/31.doASCRMAv2,PairedPSCBS.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/31.doASCRMAv2,PairedPSCBS.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/31.doASCRMAv2,PairedPSCBS.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/launch.R | 62 +
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142/11a,doASCRMAv2.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/parallel/chipTypes/Mapping10K_Xba142/21a,doCBS.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_affyPLM.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/12.doGCRMA_vs_gcrma.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/11.MatNormalization_vs_MAT.R | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp/12.CRLMM_vs_oligo.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01a.downloadAnnotData.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/01a.downloadAnnotData.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01a.downloadAnnotData.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/11.GcRmaBgCorr.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/setup/01a.downloadAllAnnotationData.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/setup/01b.downloadAllRawDataSet.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/setup/01c.installAllPackages.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/setup/99a.cleanupRootDirectories.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,GCNorm.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plots.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/11.MatNormalization.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1,SmNorm.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,CE.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots,pairs.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01a.downloadAnnotData.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/11.RmaPlm.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA,QA.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA,paired.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/31.ASCRMA.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/41.BCN.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN,AS.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/51.ACC,merge.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/61.TCN,XYbias.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/71.doCBS,tuple.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/81.fnt.R |only
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/12.justSNPRMA,CRLMM.R | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Test3/01d.downloadRawData.R | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AbstractProbeSequenceNormalization.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AdditiveCovariatesNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffineCnPlm.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffinePlm.Rd | 12
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffineSnpPlm.Rd | 10
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 32
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixCelFile.Rd | 24
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixCelSetReporter.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixCelSetTuple.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixFile.Rd | 22
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixFileSetReporter.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixPgfFile.Rd | 32
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 24
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AlleleSummation.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AllelicCrosstalkCalibration.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 24
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ArrayExplorer.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AvgCnPlm.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AvgPlm.Rd | 12
aroma.affymetrix-2.8.0/aroma.affymetrix/man/AvgSnpPlm.Rd | 10
aroma.affymetrix-2.8.0/aroma.affymetrix/man/BackgroundCorrection.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/BaseCountNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/BasePositionNormalization.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ChipEffectFile.Rd | 33
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ChipEffectGroupMerge.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ChipEffectSet.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ChipEffectTransform.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/CnChipEffectFile.Rd | 39
aroma.affymetrix-2.8.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/CnPlm.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 41
aroma.affymetrix-2.8.0/aroma.affymetrix/man/CnagCfhFile.Rd | 24
aroma.affymetrix-2.8.0/aroma.affymetrix/man/CnagCfhSet.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/CrlmmParametersFile.Rd | 28
aroma.affymetrix-2.8.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/DChipCdfBinFile.Rd | 28
aroma.affymetrix-2.8.0/aroma.affymetrix/man/DChipDcpFile.Rd | 24
aroma.affymetrix-2.8.0/aroma.affymetrix/man/DChipDcpSet.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/DChipGenomeInformation.Rd | 20
aroma.affymetrix-2.8.0/aroma.affymetrix/man/DChipQuantileNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/DChipSnpInformation.Rd | 20
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ExonChipEffectFile.Rd | 35
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 39
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ExonRmaPlm.Rd | 10
aroma.affymetrix-2.8.0/aroma.affymetrix/man/FirmaFile.Rd | 33
aroma.affymetrix-2.8.0/aroma.affymetrix/man/FirmaModel.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/FirmaSet.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/FragmentEquivalentClassNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/FragmentLengthNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/GcContentNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/GcContentNormalization2.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/GcRmaBackgroundCorrection.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/GenericReporter.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/GenomeInformation.Rd | 20
aroma.affymetrix-2.8.0/aroma.affymetrix/man/HetLogAddCnPlm.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/HetLogAddPlm.Rd | 12
aroma.affymetrix-2.8.0/aroma.affymetrix/man/HetLogAddSnpPlm.Rd | 10
aroma.affymetrix-2.8.0/aroma.affymetrix/man/LimmaBackgroundCorrection.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/LinearModelProbeSequenceNormalization.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/MatNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/MatSmoothing.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/MbeiCnPlm.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/MbeiPlm.Rd | 12
aroma.affymetrix-2.8.0/aroma.affymetrix/man/MbeiSnpPlm.Rd | 10
aroma.affymetrix-2.8.0/aroma.affymetrix/man/Model.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/MultiArrayUnitModel.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/Non-documented_objects.Rd | 13
aroma.affymetrix-2.8.0/aroma.affymetrix/man/NormExpBackgroundCorrection.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/OpticalBackgroundCorrection.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ParameterCelFile.Rd | 30
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ParameterCelSet.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ProbeAffinityFile.Rd | 33
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ProbeLevelModel.Rd | 10
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ProbeLevelTransform.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ProbeLevelTransform3.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/QualityAssessmentFile.Rd | 26
aroma.affymetrix-2.8.0/aroma.affymetrix/man/QualityAssessmentModel.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/QuantileNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ReseqCrosstalkCalibration.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ResidualFile.Rd | 33
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ResidualSet.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/RmaBackgroundCorrection.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/RmaCnPlm.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/RmaPlm.Rd | 12
aroma.affymetrix-2.8.0/aroma.affymetrix/man/RmaSnpPlm.Rd | 10
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ScaleNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/ScaleNormalization3.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SingleArrayUnitModel.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SmoothMultiarrayModel.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SmoothRmaModel.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SnpChipEffectFile.Rd | 35
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SnpChipEffectGroupMerge.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SnpInformation.Rd | 20
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SnpPlm.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 39
aroma.affymetrix-2.8.0/aroma.affymetrix/man/SpatialReporter.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/TransformReport.Rd | 2
aroma.affymetrix-2.8.0/aroma.affymetrix/man/UgpGenomeInformation.Rd | 20
aroma.affymetrix-2.8.0/aroma.affymetrix/man/UnitModel.Rd | 6
aroma.affymetrix-2.8.0/aroma.affymetrix/man/UnitTypeScaleNormalization.Rd | 4
aroma.affymetrix-2.8.0/aroma.affymetrix/man/WeightsFile.Rd | 33
aroma.affymetrix-2.8.0/aroma.affymetrix/man/WeightsSet.Rd | 8
aroma.affymetrix-2.8.0/aroma.affymetrix/man/byChipType.AromaChipTypeAnnotationFile.Rd | 5
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.ChipEffectFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.CnChipEffectFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.CnProbeAffinityFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.ExonChipEffectFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.ExonProbeAffinityFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.FirmaFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.ProbeAffinityFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.ResidualFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.SnpChipEffectFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.SnpProbeAffinityFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/getCellIndices.WeightsFile.Rd |only
aroma.affymetrix-2.8.0/aroma.affymetrix/man/writeCdf.AffyGenePDInfo.Rd | 15
302 files changed, 2477 insertions(+), 1222 deletions(-)
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-09-29 0.3-136
2011-07-23 0.3-67
2010-08-27 0.3-38
2010-08-13 0.3-33
2010-08-12 0.3-30
2010-08-11 0.3-27
2010-08-09 0.3-19
2010-07-09 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-01-08 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-24 1.1
2012-03-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-10-19 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-12-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-03-01 1.2
2009-12-23 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-17 1.3
2011-06-20 1.2
2010-01-14 1.1
2009-08-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-06-28 1.3-25
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-01-03 1.1
2008-01-16 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-02 1.2.1
2012-05-14 1.2
2012-04-24 1.1
2012-03-22 1.0
Title: MetaQC: Objective Quality Control and Inclusion/Exclusion
Criteria for Genomic Meta-Analysis
Diff between MetaQC versions 0.1.12 dated 2012-11-15 and 0.1.13 dated 2012-12-22
Description: MetaQC implements our proposed quantitative quality
control measures: (1) internal homogeneity of co-expression
structure among studies (internal quality control; IQC); (2)
external consistency of co-expression structure correlating
with pathway database (external quality control; EQC); (3)
accuracy of differentially expressed gene detection (accuracy
quality control; AQCg) or pathway identification (AQCp); (4)
consistency of differential expression ranking in genes
(consistency quality control; CQCg) or pathways (CQCp). (See
the reference for detailed explanation.) For each quality
control index, the p-values from statistical hypothesis testing
are minus log transformed and PCA biplots were applied to
assist visualization and decision. Results generate systematic
suggestions to exclude problematic studies in microarray
meta-analysis and potentially can be extended to GWAS or other
types of genomic meta-analysis. The identified problematic
studies can be scrutinized to identify technical and biological
causes (e.g. sample size, platform, tissue collection,
preprocessing etc) of their bad quality or irreproducibility
for final inclusion/exclusion decision.
Author: Don Kang
Maintainer: Don Kang
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/MetaQC.R | 4 ++--
man/MetaQC-package.Rd | 4 ++--
4 files changed, 11 insertions(+), 11 deletions(-)
Title: Functions for re-sampling a community matrix to compute
diversity indices at different sampling levels.
Diff between DiversitySampler versions 2.0 dated 2009-12-10 and 2.1 dated 2012-12-22
More information about DiversitySampler at CRAN
Description: There are two functions in this package, which can be used
together to estimate the Shannon's Diversity index at different
levels of sample size. A Monte-Carlo procedure is used to
re-sample a given observation at each level of sampling. The
expectation being that the mean of the re-sampling will
approach Shannon's diversity index at that sample level.
Author: Matthew K. Lau
Maintainer: Matthew K. Lau
DESCRIPTION | 10 +++++-----
MD5 |only
NAMESPACE |only
man/DiversitySampler-package.Rd | 4 ++--
man/Gd.Rd | 2 +-
man/H.sampler.Rd | 4 ++--
man/Hs.Rd | 2 +-
man/count.Rd | 6 +++---
8 files changed, 14 insertions(+), 14 deletions(-)
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-08-01 1.3-0
2008-04-08 1.2-5
2008-04-02 1.2-4
2008-02-22 1.2-2
2008-02-22 1.2-3
2008-02-21 1.2-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-01 1.1.11
2012-09-04 1.1.10
2012-07-16 1.1.8
2012-07-16 1.1.9
2012-03-20 1.1.6
2012-03-13 1.1.5
2012-02-16 1.1.4
2012-02-14 1.1.3
2012-02-13 1.1.2
2012-01-27 1.0.11
2011-11-10 1.0.7
2011-10-14 1.0.5
2011-09-21 1.0.3
2011-09-16 1.0.0
2011-09-16 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-02-19 2.11.1-1.0.1
2011-02-17 2.11.1-1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-12-19 0.8-6
2009-05-24 0.8-5
2009-02-25 0.8-4
2008-09-19 0.8-3
2008-09-16 0.8-2
2008-06-19 0.8-1
2008-06-12 0.8
2008-06-10 0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-12-16 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-03-13 0.1-2
2009-02-10 0.1-1
2009-02-03 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-08-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-04-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-08-09 2.12-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-05-08 1.0.1
Title: Bindings for the Geospatial Data Abstraction Library
Diff between rgdal versions 0.7-25 dated 2012-12-09 and 0.8-01 dated 2012-12-22
Description: Provides bindings to Frank Warmerdam's Geospatial Data
Abstraction Library (GDAL) (>= 1.7.1) and access to
projection/transformation operations from the PROJ.4 library.
The GDAL and PROJ.4 libraries are external to the package, and,
when installing the package from source, must be correctly
installed first. Both GDAL raster and OGR vector map data can
be imported into R, and GDAL raster data and OGR vector data
exported. Use is made of classes defined in the sp package.
Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and
Expat) are provided on CRAN.
Author: Timothy H. Keitt
Maintainer: Roger Bivand
ChangeLog | 78
DESCRIPTION | 14
MD5 | 56
NAMESPACE | 2
R/AAA.R | 2
R/Class-CRSx.R | 10
R/gdal.R | 39
R/ogr.R | 18
R/ogr_sp.R | 37
R/project.R | 2
configure | 5359 +++++++++++++++++++++--------------------------
configure.ac | 6
inst/ChangeLog | 78
inst/README | 17
inst/SVN_VERSION | 2
inst/doc |only
inst/etc |only
man/GDALDataset-class.Rd | 2
man/GDALDriver-class.Rd | 6
man/readOGR.Rd | 9
man/writeOGR.Rd | 2
src/gdal-bindings.cpp | 43
src/init.c | 3
src/projectit.cpp | 16
src/rgdal.h | 5
tests/tests.Rout.save | 6
vignettes |only
27 files changed, 2848 insertions(+), 2964 deletions(-)