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).

AuthorPeter M. Haverty
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

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

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