vcf2lfmm {LEA} | R Documentation |
vcf
to lfmm
formatA function that converts from the vcf
format to the
lfmm
format.
vcf2lfmm(input.file, output.file = NULL, force = TRUE)
input.file |
A character string containing a path to the input file,
a genotypic matrix in the |
output.file |
A character string containing a path to the output file,
a genotypic matrix in the |
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. |
output.file |
A character string containing a path to the output file,
a genotypic matrix in the |
Eric Frichot
vcf
lfmm.data
ancestrymap2lfmm
ancestrymap2geno
ped2lfmm
ped2geno
vcf2geno
# 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 lfmm format ("example.lfmm"). # By default, the name of the output file is the same name # as the input file with a .lfmm extension. # Create files: "example.lfmm", # "example.vcfsnp" - SNP informations, # "example.removed" - removed lines. output = vcf2lfmm("example.vcf") # Conversion from the vcf format ("example.vcf") # to the lfmm format with the output file called "plop.lfmm". # Create files: "plop.lfmm", # "plop.vcfsnp" - SNP informations, # "plop.removed" - removed lines. output = vcf2lfmm("example.vcf", "plop.lfmm") # As force = false and the file "example.lfmm" already exists, # nothing happens. output = vcf2lfmm("example.vcf", force = FALSE)