Man pages for genoset
A RangedSummarizedExperiment with methods for copy number analysis

baf2mbafCalculate mBAF from BAF
boundingIndicesFind indices of features bounding a set of chromosome...
boundingIndicesByChrFind indices of features bounding a set of chromosome...
bounds2RleConvert bounding indices into a Rle
calcGCCalculate GC Percentage in windows
calcGC2Calculate GC Percentage in sliding window
chrIndices-methodsGet a matrix of first and last index of features in each...
chrInfo-methodsGet chromosome start and stop positions
chr-methodsChromosome name for each feature
chrNames-methodsGet list of unique chromosome names
chrOrderOrder chromosome names in proper genome order
chrPartitioningPartitioning by Chromosome
cn2lr-methodsTake vector or matrix of copynumber values, convert to...
do_rledf_range_summaryCalculate min/max/sum/mean/whichmin/whichmax over ranges on...
do_rledf_viewsCalculate min/max/sum/mean/whichmin/whichmax over each view...
fixSegNAsFix NA runs in a Rle
gcCorrectCorrect copy number for GC content
genomeGet and set the genome universe annotation.
genomeAxisLabel axis with base pair units
genomicranges-methodsGenomicRanges API Additions
genoPlot-methodsPlot data along the genome
genoPos-methodsGet base positions of features in genome-scale units
GenoSet-classClass '"GenoSet"'
genoset-datasetExample GenoSet object
genoset-methodsCreate a GenoSet object
genoset-packageGenoSet: An eSet for data with genome locations
genoset-subsetSubset a GenoSet
isGenomeOrderCheck if a GRanges orGenoSet is in genome order
lr2cnTake vector or matrix of log2 ratios, convert to copynumber
modeCenterCenter continuous data on mode
numCallableCount Rle positions >= min
pos-methodsChromosome position of features
rangeSampleMeansAverage features in ranges per sample
rangeSegMeanLength-methodsGet segment widths
rbindDataframeA fast method for concatenating data.frames
readGenoSetLoad a GenoSet from a RData file
RleDataFrame-classClass '"RleDataFrame"'
RleDataFrame-viewsCalculate summary statistics on views of an RleDataFrame
runCBSRun CBS Segmentation
segPairTable-methodsConvert Rle objects to tables of segments
segs2GrangesGRanges from segment table
segs2RleMake Rle from segments for one sample
segs2RleDataFrameCBS segments to probe matrix
segTable-methodsConvert Rle objects to tables of segments
toGenomeOrderSet a GRanges or GenoSet to genome order
genoset documentation built on Nov. 8, 2020, 6:07 p.m.