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Transforms segment tables into per-bin copy-number tables.

SegmentsToCopyNumber.Rd

SegmentsToCopyNumber() transforms segment tables into per-bin copy-number tables. It is an expansion of the calls into per-bin style, where the bin size is user defined. It is the inverse of the CopyNumberSegments function.

Usage

SegmentsToCopyNumber(segs, bin_size, genome = "hg19", Xincluded = FALSE)

Arguments

segs

A list of dataframes, where each dataframe is a dataframe of the segmented copy-numbers.

bin_size

A natural number. The binsize used in the copy number object, ex. 30 -> 30kb, 100 -> 100kb.

genome

A string. Refers to the reference genome, common reference genomes are: 'hg19', 'mm10', or 'hg38'.

Xincluded

A boolean. Sex chromosomes as a Boolean (e.g. FALSE if not included).

Value

A dataframe of per-bin copy numbers (bounded for each sample).