Description Usage Arguments Value Author(s)
convenience function to convert genotypes from .vcf files to the MatrixEQTL format
1 2 | convert.vcf(vcf.file, which = "GT", map = FALSE, snp.pos = FALSE,
genotype_file_name = NULL)
|
vcf.file |
vcf.file containing genotypes |
which |
which field of the .vcf file to use: "GT" = genotype, "DS" = genotype dosage from MaCH/Thunder, "GL" = genotype likelihoods (default "GT") |
map |
should the map object extracted from |
snp.pos |
names for colums with annotations for custom build, order: chromosome (chr), length (pos) (default NULL) |
genotype_file_name |
either a matrix nsnps x nsample containing genotypes coded as 0,1,2 or a list with slots "gt.mat", "map", "snp.pos"
Ines Assum (2019-03-21)
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