filterSeg: Filter segments

In MPAgenomics: Multi-Patient Analysis of Genomic Markers

Description

This function filters the output of a segmentation and label process. It allows to keep only segments over a minimal length or containing at least a minimal number of probes.

Usage

filterSeg(segmentList, minLength = 1, minProbes = 1, keptLabel = c("loss",
  "gain"))

Arguments

segmentList	A data.frame containing a description of segments, it must have at least columns named "chromStart", "chromEnd", "probes" and "calls". (see the output of cnSegCallingProcess function).
minLength	The minimum length (in bp) for a segment. All the shorter segments are removed.
minProbes	The minimum number of probes for a segment. All the segments with less probes are removed.
keptLabel	Vector of labels to keep. Only segment with one of the specified label will be kept.

Value

a data.frame of the same format as segmentList.

Author(s)

Quentin Grimonprez

MPAgenomics documentation built on Jan. 16, 2020, 3 p.m.