tn.norm.qc.div: Targeted normalization QC: diversity of the supporting bins

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

Description

Computes the diversity of the supporting bins used during normalization. For now it only computes the number of bins in the same chromosome as the bin to normalize. To avoid over-normalization of large CNVs or full-chromosome aneuploidy (e.g. in cancer), we would like the majority of the supporting to be located different chromosomes than the bin to normalize.

Usage

tn.norm.qc.div(norm.stats, out.pdf = "normStats-QC-supportDiversity.pdf",
  chunk.size = 1000, nb.cores = 1)

Arguments

norm.stats	the name of the file with the normalization statistics ('norm.stats' in 'tn.norm' function) or directly a 'norm.stats' data.frame.
out.pdf	the name of the PDF file to create.
chunk.size	the size of a chunk to read the file. Default is 1000.
nb.cores	the number of cores to use. Default is 1.

Value

a data.frame with the bins location and the computed metric.

Author(s)

Jean Monlong

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