correct.GC: Correct GC bias

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Correct GC bias by fitting a LOESS model. The bin counts are then corrected with a continuous normalization factor derived from the predicted bin count and global average bin count.

Usage

correct.GC(bc.f, gc.df, outfile.prefix, appendIndex.outfile = TRUE)

Arguments

bc.f	the name of the file with the bin count for a particular sample OR a data.frame with 4 columns: 'chr', 'start', 'end' and 'bc'.
gc.df	a data.frame with the bin definition and GC content information. Column 'GCcontent' is required and can be obtained thanks to 'getGC.hg19' for example.
outfile.prefix	the prefix for the output file name. The suffix '.bgz' will be appended to this name prefix after compression.
appendIndex.outfile	if TRUE (default), the results will be saved on the output file which will be ultimately compressed/indexed. This is recommend when a large number of bins are analyzed. If FALSE, a data.frame with the corrected bin counts will be returned and no file is created.

Value

the name of the file with the corrected bin counts OR a new data.frame with corrected bin counts.

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.