filter_called: Filter the Called snp array

In LieberInstitute/brainstorm_package: Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

Filter the Called snp array

Description

Filter the Called snp array

Usage

filter_called(
  called,
  DP_min = 5,
  DP_max = 80,
  ref_call = 1,
  alt_call = 1,
  overlaps = 1,
  min_VDB = 0.1
)

Arguments

called	CollapsedVCF containing filtered snp info for rna data
DP_min	TODO
DP_max	TODO
ref_call	TODO
alt_call	TODO
overlaps	TODO
min_VDB	TODO

Value

Filtered snp array

Examples

dim(snpsCalled_VCF)
snpsCalled_filter <- filter_called(snpsCalled_VCF)
dim(snpsCalled_filter)

LieberInstitute/brainstorm_package documentation built on Dec. 14, 2024, 10:29 p.m.