R: Convert from 'vcf' to 'geno' format

vcf2geno {LEA}

R Documentation

Convert from `vcf` to `geno` format

Description

A function that converts from the vcf format to the geno format.

Usage

vcf2geno(input.file, output.file = NULL, force = TRUE)

Arguments

`input.file`	A character string containing a path to the input file, a genotypic matrix in the `vcf` format.
`output.file`	A character string containing a path to the output file, a genotypic matrix in the `geno` format. By default, the name of the output file is the same name as the input file with a .geno extension.
`force`	A boolean option. If FALSE, the input file is converted only if the output file does not exist. If TRUE, convert the file anyway.

Value

output.file

A character string containing a path to the output file, a genotypic matrix in the geno format.

Author(s)

Eric Frichot

Examples

# Creation of a file called "example.vcf"
# with 4 SNPs for 3 individuals.
data("example_vcf")
write.table(example_vcf,"example.vcf",col.names =
    c("#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO",
    "FORMAT", "SAMPLE0", "SAMPLE1", "SAMPLE2"),
    row.names = FALSE, quote = FALSE)

# Conversion    from the vcf format ("example.vcf") 
#               to the geno format ("example.geno").
# By default,   the name of the output file is the same name
#               as the input file with a .geno extension.
# Create files: "example.geno",
#               "example.vcfsnp" - SNP informations,
#               "example.removed" - removed lines. 
output = vcf2geno("example.vcf")

# Conversion    from the vcf format ("example.vcf")
#               to the geno format with the output file called "plop.geno".
# Create files: "plop.geno",
#               "plop.vcfsnp" - SNP informations,
#               "plop.removed" - removed lines. 
output = vcf2geno("example.vcf", "plop.geno")

# As force = false and the file "example.geno" already exists,
# nothing happens.
output = vcf2geno("example.vcf", force = FALSE)

[Package LEA version 2.4.0 Index]

Convert from vcf to geno format