clean.cnv.artifact: CNV artifact detection and filtering

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

Description

Detects identical or near-identical CNV segments across multiple samples susceptible of representing common variants or technical artifacts. Then those segments CNV log-ratio is replaced by the flanking segments average

Usage

clean.cnv.artifact(
  cnv,
  n.reps = 4,
  cnv.size = 2e+06,
  pc.overlap = 0.99,
  fill.gaps = TRUE,
  minsize = 5000,
  verbose = TRUE
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
n.reps	(numeric) number of samples with identical segment to consider artifact
cnv.size	(numeric) only smaller segments will be modified in the cnv data.frame
pc.overlap	(numeric) minimun percentage overlap for a pair of segments to be consider identical
fill.gaps	(logical) whether to fill gaps from the segmentaed file after filtering artifacts
minsize	(numeric) the minimum gap size required to fill the gap. Only used if 'fill.gaps=TRUE'
verbose	(logical) whether to print internal messages

Value

a data.frame containing CNV data

Examples

## validate input data.frame
cnv <- validate.cnv(segdat_lung_ccle)

cnvcl <- clean.cnv.artifact(cnv)
cnvcl

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.