Convert from ancestrymap to geno format

Description

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

Usage

ancestrymap2geno(input.file, output.file = NULL, force = TRUE)

Arguments

Value

Author(s)

Eric Frichot

See Also

ancestrymap geno read.geno ancestrymap2lfmm geno2lfmm ped2lfmm ped2geno vcf2geno lfmm2geno

Examples

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

# Conversion    from the ancestrymap format ("example.ancestrymap") 
#               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 file:  "example.geno".
output = ancestrymap2geno("example.ancestrymap")

# Conversion    from the ancestrymap format (example.ancestrymap) 
#               to the geno format with the output file called plop.geno.
# Create file:  "plop.geno".
output = ancestrymap2geno("example.ancestrymap", "plop.geno")

# As force = false and the file "example.geno" already exists,
# nothing happens.
output = ancestrymap2geno("example.ancestrymap", force = FALSE)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LEA)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LEA/ancestrymap2geno.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ancestrymap2geno
> ### Title: Convert from 'ancestrymap' to 'geno' format
> ### Aliases: ancestrymap2geno
> ### Keywords: conversion
> 
> ### ** Examples
> 
> # Creation of of file called "example.ancestrymap"
> # a file containing 4 SNPs for 3 individuals.
> data("example_ancestrymap")
> write.table(example_ancestrymap,"example.ancestrymap",
+ col.names = FALSE, row.names = FALSE, quote = FALSE)
> 
> # Conversion    from the ancestrymap format ("example.ancestrymap") 
> #               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 file:  "example.geno".
> output = ancestrymap2geno("example.ancestrymap")

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

> 
> # Conversion    from the ancestrymap format (example.ancestrymap) 
> #               to the geno format with the output file called plop.geno.
> # Create file:  "plop.geno".
> output = ancestrymap2geno("example.ancestrymap", "plop.geno")

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

> 
> # As force = false and the file "example.geno" already exists,
> # nothing happens.
> output = ancestrymap2geno("example.ancestrymap", force = FALSE)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>