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

readVCFToListByRange {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

    readVCFToListByRange(fileName, range, annoType, vcfColumn, vcfInfo,
      vcfIndv)

### Arguments

`fileName` | character, represents an input VCF file (Bgzipped, with Tabix index)
`range` | character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index
`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")
    cfh <- readVCFToListByRange(fileName, "1:196621007-196716634", "Nonsynonymous",
                                c("CHROM", "POS"), c("AF", "AC"), c("GT") )

[Package seqminer version 8.0 Index]