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

readVCFToListByGene {seqminer} | R Documentation

## 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") )

[Package seqminer version 8.0 Index]