genoset: A RangedSummarizedExperiment with methods for copy number analysis
Version 1.32.0

GenoSet provides an extension of the RangedSummarizedExperiment class with additional API features. This class provides convenient and fast methods for working with segmented genomic data. Additionally, GenoSet provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome).

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AuthorPeter M. Haverty
Bioconductor views CopyNumberVariation DataRepresentation Infrastructure Microarray SNP
Date of publicationNone
MaintainerPeter M. Haverty <phaverty@gene.com>
LicenseArtistic-2.0
Version1.32.0
URL https://github.com/phaverty/genoset
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genoset")

Man pages

baf2mbaf: Calculate mBAF from BAF
boundingIndices: Find indices of features bounding a set of chromosome...
boundingIndicesByChr: Find indices of features bounding a set of chromosome...
bounds2Rle: Convert bounding indices into a Rle
calcGC: Calculate GC Percentage in windows
calcGC2: Calculate GC Percentage in sliding window
chrIndices-methods: Get a matrix of first and last index of features in each...
chrInfo-methods: Get chromosome start and stop positions
chr-methods: Chromosome name for each feature
chrNames-methods: Get list of unique chromosome names
chrOrder: Order chromosome names in proper genome order
chrPartitioning: Partitioning by Chromosome
cn2lr-methods: Take vector or matrix of copynumber values, convert to...
do_rledf_range_summary: Calculate min/max/sum/mean/whichmin/whichmax over ranges on...
do_rledf_views: Calculate min/max/sum/mean/whichmin/whichmax over each view...
fixSegNAs: Fix NA runs in a Rle
gcCorrect: Correct copy number for GC content
genome: Get and set the genome universe annotation.
genomeAxis: Label axis with base pair units
genomicranges-methods: GenomicRanges API Additions
genoPlot-methods: Plot data along the genome
genoPos-methods: Get base positions of features in genome-scale units
GenoSet-class: Class '"GenoSet"'
genoset-dataset: Example GenoSet object
genoset-methods: Create a GenoSet object
genoset-package: GenoSet: An eSet for data with genome locations
genoset-subset: Subset a GenoSet
isGenomeOrder: Check if a GRanges orGenoSet is in genome order
lr2cn: Take vector or matrix of log2 ratios, convert to copynumber
modeCenter: Center continuous data on mode
numCallable: Count Rle positions >= min
pos-methods: Chromosome position of features
rangeSampleMeans: Average features in ranges per sample
rangeSegMeanLength-methods: Get segment widths
rbindDataframe: A fast method for concatenating data.frames
readGenoSet: Load a GenoSet from a RData file
RleDataFrame-class: Class '"RleDataFrame"'
RleDataFrame-views: Calculate summary statistics on views of an RleDataFrame
runCBS: Run CBS Segmentation
segPairTable-methods: Convert Rle objects to tables of segments
segs2Granges: GRanges from segment table
segs2Rle: Make Rle from segments for one sample
segs2RleDataFrame: CBS segments to probe matrix
segTable-methods: Convert Rle objects to tables of segments
toGenomeOrder: Set a GRanges or GenoSet to genome order

Functions

.do_rledf_range_summary Man page
.do_rledf_views Man page
GenoSet Man page Source code
GenoSet-class Man page
GenoSetOrGenomicRanges-class Man page
RleDataFrame Man page Source code
RleDataFrame-class Man page
RleDataFrame-views Man page
[,GenoSet,ANY-method Man page
[<-,GenoSet,ANY,ANY,ANY-method Man page
as.matrix,RleDataFrame-method Man page
baf2mbaf Man page Source code
boundingIndices Man page Source code
boundingIndicesByChr Man page Source code
bounds2Rle Man page Source code
calcGC Man page Source code
calcGC2 Man page Source code
chr Man page
chr,GenoSet-method Man page
chr,GenomicRanges-method Man page
chrIndices Man page
chrIndices,GenoSetOrGenomicRanges-method Man page
chrInfo Man page
chrInfo,GenoSetOrGenomicRanges-method Man page
chrNames Man page
chrNames,GenoSet-method Man page
chrNames,GenomicRanges-method Man page
chrNames<- Man page
chrNames<-,GenoSet-method Man page
chrNames<-,GenomicRanges-method Man page
chrOrder Man page Source code
chrPartitioning Man page Source code
cn2lr Man page
cn2lr,DataFrame-method Man page
cn2lr,matrix-method Man page
cn2lr,numeric-method Man page
coerce,RleDataFrame,matrix-method Man page
colMeans,DataFrame-method Man page
colMeans,RleDataFrame-method Man page
colSums,RleDataFrame-method Man page
do_rledf_range_summary Source code
do_rledf_views Source code
fixSegNAs Man page Source code
gcCorrect Man page Source code
genoPlot Man page
genoPlot,GenoSetOrGenomicRanges,ANY-method Man page
genoPlot,numeric,Rle-method Man page
genoPlot,numeric,numeric-method Man page
genoPos Man page
genoPos,GenoSetOrGenomicRanges-method Man page
genome Man page
genomeAxis Man page Source code
genoset Man page
genoset-datasets Man page
genoset-package Man page
genoset.ds Man page
isGenomeOrder Man page Source code
lengths,GenoSet-method Man page
lr2cn Man page Source code
modeCenter Man page Source code
nrow,GenomicRanges-method Man page
numCallable Man page Source code
pos,GenoSetOrGenomicRanges-method Man page
rangeColMeans Man page Source code
rangeMaxs Man page
rangeMaxs,RleDataFrame-method Man page
rangeMeans Man page
rangeMeans,RleDataFrame-method Man page
rangeMeans,matrix-method Man page
rangeMeans,numeric-method Man page
rangeMins Man page
rangeMins,RleDataFrame-method Man page
rangeSampleMeans Man page Source code
rangeSegMeanLength Man page Source code
rangeSegMeanLength,GRanges,data.frame-method Man page
rangeSegMeanLength,GRanges,list-method Man page
rangeSums Man page
rangeSums,RleDataFrame-method Man page
rangeWhichMaxs Man page
rangeWhichMaxs,RleDataFrame-method Man page
rangeWhichMins Man page
rangeWhichMins,RleDataFrame-method Man page
rbindDataframe Man page Source code
readGenoSet Man page Source code
rle_range_means Source code
rle_view_maxs Source code
rle_view_means Source code
rle_view_mins Source code
rle_view_sums Source code
rle_view_which_maxs Source code
rle_view_which_mins Source code
rowMeans,RleDataFrame-method Man page
rowSums,RleDataFrame-method Man page
runCBS Man page Source code
segPairTable Man page
segPairTable,DataFrame,DataFrame-method Man page
segPairTable,Rle,Rle-method Man page
segTable Man page
segTable,DataFrame-method Man page
segTable,Rle-method Man page
segs2Granges Man page Source code
segs2Rle Man page Source code
segs2RleDataFrame Man page Source code
show,RleDataFrame-method Man page
test Source code
toGenomeOrder Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/RleDataFrame-class.R
R/RleDataFrame-methods.R
R/bounds.R
R/genoset-class.R
R/ordering.R
R/plots.R
R/rangeSummaries.R
R/segments.R
R/test_genoset_package.R
R/utils.R
TODO
build
build/vignette.rds
data
data/genoset.RData
inst
inst/NEWS
inst/NEWS.old
inst/doc
inst/doc/genoset.R
inst/doc/genoset.Rmd
inst/doc/genoset.html
inst/scripts
inst/scripts/make.fake.genoset.data.R
inst/unitTests
inst/unitTests/test_DataFrame.R
inst/unitTests/test_RleDataFrame-views.R
inst/unitTests/test_bounds.R
inst/unitTests/test_c_utils.R
inst/unitTests/test_genoset-class.R
inst/unitTests/test_locations.R
inst/unitTests/test_plots.R
inst/unitTests/test_segments.R
inst/unitTests/test_utils.R
man
man/GenoSet-class.Rd
man/RleDataFrame-class.Rd
man/RleDataFrame-views.Rd
man/baf2mbaf.Rd
man/boundingIndices.Rd
man/boundingIndicesByChr.Rd
man/bounds2Rle.Rd
man/calcGC.Rd
man/calcGC2.Rd
man/chr-methods.Rd
man/chrIndices-methods.Rd
man/chrInfo-methods.Rd
man/chrNames-methods.Rd
man/chrOrder.Rd
man/chrPartitioning.Rd
man/cn2lr-methods.Rd
man/do_rledf_range_summary.Rd
man/do_rledf_views.Rd
man/fixSegNAs.Rd
man/gcCorrect.Rd
man/genoPlot-methods.Rd
man/genoPos-methods.Rd
man/genome.Rd
man/genomeAxis.Rd
man/genomicranges-methods.Rd
man/genoset-dataset.Rd
man/genoset-methods.Rd
man/genoset-package.Rd
man/genoset-subset.Rd
man/isGenomeOrder.Rd
man/lr2cn.Rd
man/modeCenter.Rd
man/numCallable.Rd
man/pos-methods.Rd
man/rangeSampleMeans.Rd
man/rangeSegMeanLength-methods.Rd
man/rbindDataframe.Rd
man/readGenoSet.Rd
man/runCBS.Rd
man/segPairTable-methods.Rd
man/segTable-methods.Rd
man/segs2Granges.Rd
man/segs2Rle.Rd
man/segs2RleDataFrame.Rd
man/toGenomeOrder.Rd
src
src/bounds.c
src/genoset.h
src/init.c
src/rangeSummaries.c
src/utils.c
tests
tests/prove.R
tests/prove.Rout.save
vignettes
vignettes/genoset.Rmd
genoset documentation built on May 20, 2017, 11:02 p.m.