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 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
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. In addition, you can use the
qtlcart.mcd files that were formatted for the Windows version of
Rcross can read the input files formatted for use with PLABQTL.
You will need to add the phrase -filetype plabqtl0.inp (matrix format)
or -filetype plabqtl1.inp (vector format)
to the first line of the PLABQTL formatted input file. Also, be sure that
there are no map files in the current working directory: You want Rcross to
read the map that is in the PLABQTL input file. If your PLABQTL input file
has measurements for your traits in different environments, you need to add the
phrase -environments x at the end of the first line, where x is the number of
environments. If you have t traits, then Rcross will output (x+1)t
traits. Generally, the main block of data will have the means of each trait over
environments while the raw data are appended to the end of the PLABQTL file.
The raw measurements will be named TrYEnvX in the output, where Y and
X are the trait and environment numbers. For example, if weight (trait 1) and height (trait 2)
are the two traits and they are measured in three environments, then there will
be eight traits in the output file. The raw data for weight will be named
Tr1Env1, Tr1Env2 and Tr1Env3, while for height they will be Tr2Env1,
Tr2Env2 and Tr2Env3.
Rcross can produce eight different types of output files. The output formats
are specified by an integer from 0 to 7 used with the -g command line option or
set in the text menu. The numbers correspond to the following output formats:
This format is suitable for import into the programs R or Splus. All the data
will be written into the file and embedded in commands that allow R/Splus to
read it. In addition, Rcross writes a set of commands to do ANOVA analyses of each trait
on each marker and categorical trait. For a file named qtlcart.r, use the command
source(``qtlcart.r'') in R/Splus to import the data. Note that names of traits, markers and
categorical traits must conform to R/Splus usage.
This format is a SAS program that has all the data and a set of PROC GLM commands to do
ANOVA and Means analyses similiar to the R/Splus option above. Note that names of traits, markers and
categorical traits must conform to SAS usage. Thanks to Emilio Carbonell for the suggestion.
This will produce a file suitable for input into the Windows GUI version of QTL Cartographer
(Wang, et al., 2002).
This is a single file with the genetic linkage map and the data set. The format is similar
to the map.inp and cross.inp formats.
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 uses the general genetic model developed by Cockerham (1954).
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.
Cockerham, C. C. (1954) An extension of the concept of partitioning hereditary
variance for analysis of covariances among relatives when epistasis is present.
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.
Utz, H.F. and A.E. Melchinger (1996) PLABQTL: Aprogram for composite interval
mapping of QTL. J. Agric. Genomics2(1).
Wang, S., C. J. Basten and Z.-B. Zeng (2002) Windows QTL Cartographer: WinQtlCart V2.0.
Christopher J. Basten, B. S. Weir and Z.-B. Zeng
Bioinformatics Research Center, North Carolina State University
1523 Partners II Building/840 Main Campus Drive
Raleigh, NC 27695-7566 USA