genoset: A RangedSummarizedExperiment with methods for copy number analysis

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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genoset")
AuthorPeter M. Haverty
Bioconductor views CopyNumberVariation DataRepresentation Infrastructure Microarray SNP
Date of publicationNone
MaintainerPeter M. Haverty <phaverty@gene.com>
LicenseArtistic-2.0
Version1.30.0
https://github.com/phaverty/genoset

View on Bioconductor

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

isGenomeOrder-methods: 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

as.matrix,RleDataFrame-method Man page
baf2mbaf Man page
boundingIndices Man page
boundingIndicesByChr Man page
bounds2Rle Man page
calcGC Man page
calcGC2 Man page
chr Man page
chr,GenomicRanges-method Man page
chr,GenoSet-method Man page
chrIndices Man page
chrIndices,GenoSetOrGenomicRanges-method Man page
chrInfo Man page
chrInfo,GenoSetOrGenomicRanges-method Man page
chrNames Man page
chrNames<- Man page
chrNames<-,GenomicRanges-method Man page
chrNames,GenomicRanges-method Man page
chrNames<-,GenoSet-method Man page
chrNames,GenoSet-method Man page
chrOrder Man page
chrPartitioning Man page
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 Man page
.do_rledf_views Man page
fixSegNAs Man page
gcCorrect Man page
genome Man page
genomeAxis Man page
genoPlot Man page
genoPlot,GenoSetOrGenomicRanges,ANY-method Man page
genoPlot,numeric,numeric-method Man page
genoPlot,numeric,Rle-method Man page
genoPos Man page
genoPos,GenoSetOrGenomicRanges-method Man page
genoset Man page
GenoSet Man page
[<-,GenoSet,ANY,ANY,ANY-method Man page
[,GenoSet,ANY-method Man page
GenoSet-class Man page
genoset-datasets Man page
genoset.ds Man page
GenoSetOrGenomicRanges-class Man page
genoset-package Man page
isGenomeOrder Man page
isGenomeOrder,GenoSet-method Man page
isGenomeOrder,GRanges-method Man page
lengths,GenoSet-method Man page
locData Man page
locData<- Man page
lr2cn Man page
modeCenter Man page
nrow,GenomicRanges-method Man page
numCallable Man page
pos,GenoSetOrGenomicRanges-method Man page
rangeColMeans Man page
rangeMaxs Man page
rangeMaxs,RleDataFrame-method Man page
rangeMeans Man page
rangeMeans,matrix-method Man page
rangeMeans,numeric-method Man page
rangeMeans,RleDataFrame-method Man page
rangeMins Man page
rangeMins,RleDataFrame-method Man page
rangeSampleMeans Man page
rangeSegMeanLength Man page
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
readGenoSet Man page
RleDataFrame Man page
RleDataFrame-class Man page
RleDataFrame-views Man page
rowMeans,RleDataFrame-method Man page
rowSums,RleDataFrame-method Man page
runCBS Man page
segPairTable Man page
segPairTable,DataFrame,DataFrame-method Man page
segPairTable,Rle,Rle-method Man page
segs2Granges Man page
segs2Rle Man page
segs2RleDataFrame Man page
segTable Man page
segTable,DataFrame-method Man page
segTable,Rle-method Man page
show,RleDataFrame-method Man page
toGenomeOrder Man page

Files

DESCRIPTION
NAMESPACE
R
R/RleDataFrame-class.R R/RleDataFrame-methods.R R/bounds.R R/deprecated.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-methods.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

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