trimSnps: Function to filter out SNPs from ExAC database

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

Function to filter out SNPs from ExAC database

Usage

trimSnps(vcf, maft = 0.1)

Arguments

vcf	readVcf object from ExAC database read over a certain range
maft	minor allele frequency cutoff for filtering

Value

snps GenomicRanges object with positions of putative heterozygous SNPs info data fram with metadata for putative heterozygous SNPs

Examples

## Not run: 
vcfFile <- "../data-raw/ExAC.r0.3.sites.vep.vcf.gz"
# Filter for SNPs over all of chr1	
testRanges <- GRanges(seqnames='1', IRanges(start = 0, width=249250621))
param = ScanVcfParam(which=testRanges)
vcf <- readVcf(vcfFile, "hg19", param=param)
temp <- trimSnps(vcf)
snps <- temp$snps
info <- temp$info
head(info)
head(snps)

## End(Not run)

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.