ped2lfmm: Convert from 'ped' to 'lfmm' format

In LEA: LEA: an R package for Landscape and Ecological Association Studies

Description

A function that converts from the ped format to the lfmm format.

Usage

ped2lfmm(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 ped format.
output.file	A character string containing a path for the output file, a genotypic matricx in the lfmm format. By default, the name of the output file is the same name as the input file with a .lfmm 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 for the output file, a genotypic matricx in the lfmm format.

Author(s)

Eric Frichot

See Also

ped lfmm.data ancestrymap2lfmm ancestrymap2geno geno2lfmm ped2geno vcf2geno lfmm2geno

Examples

# Creation of a file called "example.ped"
# with 4 SNPs for 3 individuals.
data("example_ped")
write.table(example_ped,"example.ped",
    col.names = FALSE, row.names = FALSE, quote = FALSE)

# Conversion    from the ped format ("example.ped") 
#               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 file:  "example.lfmm".
output = ped2lfmm("example.ped")

# Conversion    from the ped format ("example.ped") 
#               to the geno format with the output file called "plop.lfmm".
# Create file:  "plop.lfmm".
output = ped2lfmm("example.ped", "plop.lfmm")

# As force = false and the file "example.lfmm" already exists,
# nothing happens.
output = ped2lfmm("example.ped", force = FALSE)

Example output

	- number of detected individuals:	3
	- number of detected loci:		4


	- number of detected individuals:	3
	- number of detected loci:		4

LEA documentation built on Nov. 8, 2020, 8:19 p.m.