readVCFToListByGene: Read information from VCF file in a given range and return a...

In seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Read information from VCF file in a given range and return a list

Description

Read information from VCF file in a given range and return a list

Usage

readVCFToListByGene(
  fileName,
  geneFile,
  geneName,
  annoType,
  vcfColumn,
  vcfInfo,
  vcfIndv
)

Arguments

fileName	character, represents an input VCF file (Bgzipped, with Tabix index)
geneFile	character, a text file listing all genes in refFlat format
geneName	character vector, which gene(s) to be extracted
annoType	character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty.
vcfColumn	character vector, which vcf columns to extract. It can be chosen from CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT and etc.
vcfInfo	character vector, which should be tags in the INFO columns to extarct. Common choices include: DP, AC, AF, NS
vcfIndv	character vector, which values to extract at individual level. Common choices are: GT, GQ, GD

Value

a list of genes, and each elements has specified vcfColumn, vcfinfo, vcfIndv

See Also

http://zhanxw.com/seqminer/ for online manual and examples

Examples

fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readVCFToListByGene(fileName, geneFile, "CFH", "Synonymous",
                           c("CHROM", "POS"), c("AF", "AC"), c("GT") )

seqminer documentation built on Oct. 7, 2024, 1:15 a.m.