Create a bed.matrix from VCF files
Create a bed.matrix from a .vcf file.
read.vcf(file, max.snps, get.info = FALSE, convert.chr = TRUE,
verbose = getOption("gaston.verbose",TRUE))file |
The name of the VCF file to read |
max.snps |
The maximal number of SNPs to read |
get.info |
If |
convert.chr |
If |
verbose |
If |
The vcf format is described in https://github.com/samtools/hts-specs
In addition to the usual data in the slot @snps, the bed.matrices produced by read.vcf have
@snps$quality and @snps$filter columns corresponding to the QUAL and FILTER fields in the VCF
file. If get.info = TRUE, an additionnal column @snps$info is added, corresponding to the
INFO field.
The information about individuals in VCF files is incomplete: in the slot @ped, the columns
@ped$famid and @ped$id will both contain the sample id; sex and phenotypes will be set
to unknown.
The function currently assumes that the GT field is the first field in the genotypes format.
If it is not the case, the variants are discarded.
Hervé Perdry and Claire Dandine-Roulland
## Read vcf file (from file name)
filepath <-system.file("extdata", "LCT.vcf.gz", package="gaston")
x1 <- read.vcf( filepath )
x1Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.