
R version 2.11.0 (2010-04-22)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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.

> ######################################################################
> #
> # 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")
> 
