bounds2Rle: Convert bounding indices into a Rle

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Given a matrix of first/last indices, like from boundingIndicesByChr, and values for each range, convert to a Rle. This function takes the expected length of the Rle, n, so that any portion of the full length not covered by a first/last range will be a run with the value NA. This is typical in the case where data is segmented with CBS and some of the data to be segmented is NA.

Usage

bounds2Rle(bounds, values, n)

Arguments

bounds	matrix, two columns, with first and last index, like from boundingIndicesByChr
values	ANY, some value to be associated with each range, like segmented copy number.
n	integer, the expected length of the Rle, i.e. the number of features in the genome/target ranges processed by boundingIndicesByChr.

Value

Rle

See Also

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

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