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

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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

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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") )

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