clean.cnv.artifact: Remove likely artifacts from segmentation data and fill gaps...

In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

Description

Remove likely artifacts from segmentation data and fill gaps in segmentation data

Usage

clean.cnv.artifact(
  cnv,
  n.reps = 4,
  cnv.size = 5e+06,
  pc.overlap = 0.99,
  fill.gaps = TRUE,
  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
verbose	(logical)
fill	(logical) whether to fill gaps from the segmentaed file after filtering artifacts

Value

a data.frame containing CNV data

Examples

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

clean.cnv.artifact(cnv)

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.