Rcross - Simulate or reformat a data set.
Rcross [ -o output ] [ -i input ] [ -m mapfile ] [ -q modelfile ] [ -r repetitions ][ -c Cross ] [ -n SampleSize ] [ -H heredity ] [ -E Ve ] [ -I Interactive ]
Rcross performs a random cross or reformats a data set. Cross types include F1 backcrosses to the P1 or P2, F2 crosses produced by selfing or random mating, recombinant inbred lines as well as a few others. It simulates marker and trait data. The markers simulated come from a molecular map that could be a random one produced by Rmap, or a real one in the same format as the output of Rmap. The QTL model could be a random set produced by Rqtl or an estimated set in the same format as the output of Rqtl.
Rcross can also translate files from three different formats. If the user chooses to translate a file, then the simulation options are ignored.
See QTLcart(1) for more information on the global options -h for help, -A for automatic, -V for non-Verbose -W path for a working directory, -R file to specify a resource file, -e to specify the log file, -s to specify a seed for the random number generator and -X stem to specify a filename stem. The options below are specific to this program.
If you use this program without specifying any options, then you will get into a menu that allows you to set them interactively.
This requires a filename for output. Rcross will overwrite the file if it exists, and create a new file if it does not. If not used, then Rcross will use qtlcart.cro. This output is in a format suitable for any of the mapping programs.
This requires an input filename. This file must exist. Rcross will attempt to identify the format of the file and translate it to another format. Specifying a file with this option turns off the simulation parameters below.
Rcross requires a genetic linkage map. This option require the name of a file containing the map. It should be in the same format that Rmap outputs. The default file is qtlcart.map.
Rcross needs a genetic model to simulate a data set. It will read from the file specified by this option. The file specified should contain a genetic model in the same format as the output of Rqtl. The default file is qtlcart.qtl.
Allows the user to specify the heritability for the trait. If used, it requires a value in the range 0.0 to 1.0. It is 0.5 by default.
Allows the user to specify an environmental variance for the trait. If used, it requires a positive value and will disable the heritability. This is ignored by default.
is the flag to turn on interactive crosses. By default, it has a value of 0. To do interactive crosses, use this option with the value 1.
Allows the user to specify the type of cross. It requires a string such as B1, SF2 or RI1. See below for more on the values of the cross.
This is the sample size of the offspring. It is 200 by default and requires some integer value greater than 0 if used.
The input format of the molecular map should be the same as that of the output format from the program Rmap. The input form of the QTL data should be that of the output format from Rqtl. If an input file for the data is used, then it can have one of two formats. The first is identical to the raw files required by MAPMAKER. You must first use MAPMAKER to create a genetic map, then run the map through Rmap to reformat it, then use the map and the original raw file to reformat the data for subsequent use.
An alternative format is defined in a file cross.inp that is included with the distribution. The file can be annotated freely. Look at the cross.inp file and use it as a template for your data.
A pair of inbred parental lines (P1 and P2) that differ in the trait of
interest and marker genotypes are crossed to produce an F1 generation. All
crosses are then derived from these lines. Backcrossing to P1 is encoded by
B1, and to P2 by B2. Selfed intercrosses of generation i are encoded by
SFi. Randomly mated intercrosses of generation i are encoded by RFi.
Recombinant inbreds created by selfing have the code RI1, while those by
sib-mating are RI2. Doubled haploids have the code RI0. A test cross of an
SFi line to a Pj line is encoded by T(Bj)SFi. The QTL
Cartographer manual explains some other crosses that are possible. Note
that the UNIX shell may interpret ( and ) so they should either be quoted,
or the cross entered into the interactive menu.
% Rcross -A -V -c SF2 -n 1000
Does a selfed F2 cross with 1000 offspring using the linkage map in qtlcart.map and the model in qtlcart.qtl. The command line options -A and -V turn off the interactive menu and the verbosity mode, respectively.
% Rcross -i cross.raw
Reads from the file cross.raw, tries to determine its format, and translates it if possible. The file cross.raw could be a MAPMAKER/QTL formatted file, a cross.inp formatted file or one that is already in the Rcross.out format.
Lander, E. S., P. Green, J. Abrahamson, A. Barlow, M. Daley, S. Lincoln and L. Newburg (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1, 174-181.
If you use the interactive mode, you can print out the results of crosses. The analysis of these arbitrary crosses has not been fully integrated into the other programs.
Rmap(1), Rqtl(1), Qstats(1), LRmapqtl(1), SRmapqtl(1), Zmapqtl(1), JZmapqtl(1), Eqtl(1), Prune(1), Preplot(1), QTLcart(1)
In general, it is best to contact us via email (basten@statgen.ncsu.edu)
Christopher J. Basten, B. S. Weir and Z.-B. Zeng
Department of Statistics, North Carolina State University
Raleigh, NC 27695-8203, USA
Phone: (919)515-1934