genoset (version 1.24.0)

rangeSegMeanLength: Get segment widths

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)
"rangeSegMeanLength"(range.gr, segs)
"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, segPairTable,DataFrame,DataFrame-method, segPairTable,Rle,Rle-method; segTable, segTable,DataFrame-method, segTable,Rle-method; segs2Granges; segs2RleDataFrame; segs2Rle