formatVCF {sesame} | R Documentation

## Convert SNP from Infinium array to VCF file

### Description

Convert SNP from Infinium array to VCF file

### Usage

    formatVCF(sdf, vcf = NULL, refversion = "hg19", annoS = NULL, annoI = NULL)

### Arguments

`sdf` | SigDF
`vcf` | output VCF file path, if NULL output to console
`refversion` | reference version, currently only support
`annoS` | SNP variant annotation, download if not given
`annoI` | Infinium-I variant annotation, download if not given hg19 and hg38 in human

### Value

VCF file. If vcf is NULL, a data.frame is output to console. The data.frame does not contain VCF headers.

Note the vcf is not sorted. You can sort with awk '$1 ~ /^#/ print $0;next print $0 | "sort -k1,1 -k2,2n"'

### Examples

    sesameDataCache("EPIC") # if not done yet
    sdf <- sesameDataGet('EPIC.1.SigDF')

    annoS <- sesameDataGetAnno("EPIC/EPIC.hg19.snp_overlap_b151.rds")
    annoI <- sesameDataGetAnno("EPIC/EPIC.hg19.typeI_overlap_b151.rds")
    ## output to console
    head(formatVCF(sdf, annoS=annoS, annoI=annoI))

[Package sesame version 1.12.9 Index]