filterSVs: Filter SVs for size and regions of interest

In jmonlong/sveval: SV evaluation

Filter SVs for size and regions of interest

Description

Filter SVs for size and regions of interest

Usage

filterSVs(
  sv.gr,
  regions.gr = NULL,
  ol.prop = 0.5,
  min.size = 0,
  max.size = Inf,
  accepted.filters = NULL,
  mark.pass = FALSE
)

Arguments

sv.gr	the input SVs (e.g. read from readSVvcf)
regions.gr	the regions of interest. Ignored if NULL (default).
ol.prop	minimum proportion of sv.gr that must overlap regions.gr. Default is 0.5
min.size	the minimum SV size to be considered. Default 0.
max.size	the maximum SV size to be considered. Default is Inf.
accepted.filters	vector of the values of the FILTER field to keep. If NULL (default), all values are accepted
mark.pass	don't actually filter variants but mark the variants with a 'pass' columns. Default is FALSE.

Value

if mark.pass=FALSE (default)	a subset of sv.gr that overlaps regions.gr or in the specified size range.
if mark.pass=TRUE	the input sv.gr with a new column 'pass' to mark the variants to keep.

Author(s)

Jean Monlong

jmonlong/sveval documentation built on July 31, 2023, 7:50 p.m.