problem.coverage: problem coverage

In tdhock/PeakSegPipeline: Genome-Wide Peak Prediction Using Supervised Learning and Optimal Segmentation

Description

Ensure that coverage.bedGraph has been correctly computed for a particular genomic segmentation problem.

Usage

problem.coverage(problem.dir)

Arguments

problem.dir

Path to a directory like sampleID/problems/problemID where sampleID/coverage.bigWig contains counts of aligned reads in the entire genome, and problemID is a chrom range string like chr6_dbb_hap3:3491790-3736386 that indicates the genomic coordinates of a particular segmentation problem. If problemID/coverage.bedGraph does not exist, or its first/last lines do not match the expected problemID, then we recreate it from sampleID/coverage.bigWig.

Value

problem data.table. If necessary, the bigWigToBedGraph command line program is used to create problemID/coverage.bedGraph and then we (1) stop if there are any negative or non-integer data and (2) add lines with zero counts for missing data.

Author(s)

Toby Dylan Hocking

tdhock/PeakSegPipeline documentation built on March 3, 2020, 1:35 a.m.