genoset: A RangedSummarizedExperiment with methods for copy number analysis

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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).

Author
Peter M. Haverty
Date of publication
None
Maintainer
Peter M. Haverty <phaverty@gene.com>
License
Artistic-2.0
Version
1.30.0
URLs

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

Files in this package

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