formatVCF: Convert SNP from Infinium array to VCF file

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Convert SNP from Infinium array to VCF file

Description

Convert SNP from Infinium array to VCF file

Usage

formatVCF(sdf, anno, vcf = NULL, genome = "hg38", verbose = FALSE)

Arguments

sdf	SigDF
anno	SNP variant annotation, available at https://github.com/zhou-lab/InfiniumAnnotationV1/tree/main/Anno/EPIC EPIC.hg38.snp.tsv.gz
vcf	output VCF file path, if NULL output to console
genome	genome
verbose	print more messages

Value

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

Examples

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

## Not run: 
## download anno from
## http://zwdzwd.github.io/InfiniumAnnotation
## output to console
anno = read_tsv(sesameAnno_download("EPICv2.hg38.snp.tsv.gz"))
head(formatVCF(sdf, anno))

## End(Not run)

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.