Last data update: 2014.03.03
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oligoClasses
Package: oligoClasses
Version: 1.34.0
Title: Classes for high-throughput arrays supported by oligo and crlmm
Author: Benilton Carvalho and Robert Scharpf
Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com> and Robert Scharpf <rscharpf@jhsph.edu>
Depends: R (>= 2.14)
Imports: BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), methods,
graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7),
SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>=
1.23.2), ff, foreach, BiocInstaller, utils, S4Vectors (>=
0.9.25), RSQLite
Enhances: doMC, doMPI, doSNOW, doParallel, doRedis
Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6,
pd.genomewidesnp.5, pd.mapping50k.hind240,
pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp,
genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6),
RUnit, human370v1cCrlmm, SNPchip, VanillaICE, crlmm
Description: This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.
License: GPL (>= 2)
LazyLoad: yes
Collate: AllClasses.R AllGenerics.R utils-general.R utils-lds.R
utils-parallel.R methods-gSet.R initialize-methods.R
methods-AlleleSet.R methods-AnnotatedDataFrame.R
methods-FeatureSet.R methods-AssayData.R
methods-SnpFeatureSet.R methods-oligoSnpSet.R
methods-CopyNumberSet.R methods-CNSet.R methods-PDInfo.R
methods-RangedDataCNV.R methods-SnpSet.R
methods-GenomeAnnotatedDataFrame.R methods-BeadStudioSet.R
methods-BeadStudioSetList.R methods-gSetList.R
methods-GRanges.R methods-SummarizedExperiment.R show-methods.R
functions.R zzz.R
biocViews: Infrastructure
## Local Variables:
## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
## End:
NeedsCompilation: no
Packaged: 2016-05-04 03:02:22 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'oligoClasses' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'oligoClasses'
Creating a generic function for 'close' from package 'base' in package 'oligoClasses'
** help
*** installing help indices
converting help for package 'oligoClasses'
finding HTML links ... done
AlleleSet-class html
finding level-2 HTML links ... done
AlleleSet-methods html
AssayData-methods html
AssayDataList html
BeadStudioSet-class html
BeadStudioSetList-class html
CNSet-class html
ClassesNotExported html
CopyNumberSet-class html
CopyNumberSet-methods html
DBPDInfo-class html
FeatureSetExtensions-class html
GRanges-methods html
GenomeAnnotatedDataFrame-class html
GenomeAnnotatedDataFrameFrom-methods html
SnpSet-methods html
SnpSet2-class html
SnpSuperSet-class html
SummarizedExperiment-methods html
affyPlatforms html
annotationPackages html
assayDataList-methods html
batch html
batchStatistics html
celfileDate html
celfileName html
checkExists html
checkOrder html
chromosome-methods html
chromosome2integer html
clusterOpts html
clusterOptsDeprecated html
createFF html
data-efsExample html
data-scqsExample html
data-sfsExample html
data-sqsExample html
db html
defunct html
exprs-methods html
featureDataList-methods html
ff_matrix html
ff_or_matrix-class html
ffdf html
fileConnections html
flags html
gSet-class html
gSetList-class html
generics html
genomeBuild html
geometry-methods html
getBar html
getSequenceLengths html
i2p_p2i html
integerMatrix html
is.ffmatrix html
isPackageLoaded html
isSnp-methods html
kind html
largeObjects html
ldOpts html
length-methods html
library2 html
list.celfiles html
locusLevelData html
makeFeatureGRanges html
manufacturer-methods html
ocLapply html
oligoSetExample html
oligoSnpSet-methods html
parStatus html
pdPkgFromBioC html
platform-methods html
pmFragmentLength-methods html
position-methods html
requireAnnotation html
requireClusterPkgSetDeprecated html
sampleNames-methods html
splitVec html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligoClasses)
Making 'packages.html' ... done
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