R Under development (unstable) (2023-11-16 r85542 ucrt) -- "Unsuffered Consequences"
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> ######################################################################
> #
> # TestIO/input.R
> #
> # copyright (c) 2002, Karl W Broman
> # last modified Feb, 2002
> # first written Feb, 2002
> #
> #     This program is free software; you can redistribute it and/or
> #     modify it under the terms of the GNU General Public License,
> #     version 3, as published by the Free Software Foundation.
> # 
> #     This program is distributed in the hope that it will be useful,
> #     but without any warranty; without even the implied warranty of
> #     merchantability or fitness for a particular purpose.  See the GNU
> #     General Public License, version 3, for more details.
> # 
> #     A copy of the GNU General Public License, version 3, is available
> #     at http://www.r-project.org/Licenses/GPL-3
> #
> # This file contains code for testing the cross IO in R/qtl.
> #
> # Needed input files:
> #
> #    gen.txt, map.txt, phe.txt    [Karl's format]
> #    listeria.raw, listeria.map   [mapmaker format]
> #    listeria.raw, listeria2.map  [mapmaker format; no marker pos]
> #    listeria.csv                 [csv format] 
> #    listeria2.csv                [csv format; no marker pos] 
> #
> ######################################################################
> 
> library(qtl)
> 
> ##############################
> # Reading
> ##############################
> # Read CSV format
> csv <- read.cross("csv", "", "listeria.csv")
 --Read the following data:
	 120  individuals
	 133  markers
	 1  phenotypes
 --Cross type: f2 
Warning message:
In fixXgeno.f2(cross, alleles) :
   --Assuming that all individuals are female.

> csv2 <- read.cross("csv", "", "listeria2.csv", estimate=FALSE)
 --Read the following data:
	 120  individuals
	 133  markers
	 1  phenotypes
 --Cross type: f2 
Warning message:
In fixXgeno.f2(cross, alleles) :
   --Assuming that all individuals are female.

> 
> # Read mapmaker format
> mm <- read.cross("mm", "", "listeria.raw", "listeria.map")
 --Read the following data:
	Type of cross:          f2 
	Number of individuals:  120 
	Number of markers:      133 
	Number of phenotypes:   1 
 --Cross type: f2 
Warning message:
In fixXgeno.f2(cross, alleles) :
   --Assuming that all individuals are female.

> mm2 <- read.cross("mm", "", "listeria.raw", "listeria2.map", estimate=FALSE)
 --Read the following data:
	Type of cross:          f2 
	Number of individuals:  120 
	Number of markers:      133 
	Number of phenotypes:   1 
 --Cross type: f2 
Warning message:
In fixXgeno.f2(cross, alleles) :
   --Assuming that all individuals are female.

> 
> ##############################
> # Writing
> ##############################
> # Write in CSV format
> write.cross(csv, "csv", filestem="junk1")
> csv3 <- read.cross("csv", "", "junk1.csv", genotypes=c("AA","AB","BB","not BB","not AA"))
 --Read the following data:
	 120  individuals
	 133  markers
	 3  phenotypes
 --Cross type: f2 
> comparecrosses(csv, csv3)
	Crosses are identical.
> 
> # Write in mapmaker format
> write.cross(csv, "mm", filestem="junk2")
> 
> # Cleanup
> unlink("junk1.csv")
> unlink("junk2.raw")
> unlink("junk2.prep")
> 
> proc.time()
   user  system elapsed 
   0.42    0.10    0.51