rangeSegMeanLength-methods: Get segment widths

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

The width of a genomic segment helps inform us about the importance of a copy number value. Focal amplifications are more interesting than broad gains, for example. Given a range of interesting regions (i.e. genes) this function determines all genomics segments covered by each gene and returns the average length of the segments covered by each gene in each sample. Often only a single segment covers a given gene in a given sample.

Usage

rangeSegMeanLength(range.gr, segs)

## S4 method for signature 'GRanges,list'
rangeSegMeanLength(range.gr, segs)

## S4 method for signature 'GRanges,data.frame'
rangeSegMeanLength(range.gr, segs)

Arguments

range.gr	GRanges, genome regions of interest, usually genes
segs	data.frame of segments, like from segTable, or a list of these

Value

named vector of lengths, one per item in range.gr, or a range x length(segs) of these if segs is also list-like.

See Also

Other 'segmented data': bounds2Rle, runCBS, segPairTable, segTable, segs2Granges, segs2RleDataFrame, segs2Rle

genoset documentation built on Nov. 8, 2020, 6:07 p.m.