OUTPUT

Rcross can produce seven different types of output files. The output formats are specified by an integer from 0 to 6 used with the -g command line option or set in the text menu. The numbers correspond to the following output formats:

Value 0.

qtlcart.cro: This is the default and standard format for the analysis programs in the QTL Cartographer package.

Value 1.

cross.inp: This is a standard input format designed for Rcross. The manual has more details.

Value 2.

mapmaker.raw: This is the MAPMAKER raw file format.

Value 3.

qtlcart.r: 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.

Value 4.

qtlcart.sas: This format is a SAS program that has all the data and a set of PROC ANOVA 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.

Value 5.

plabqtl0.qdt: This will produce a file suitable for input into PLABQTL. The data will be in the matrix format. See the PLABQTL manual for more details.

Value 6.

plabqtl1.qdt: This will produce a file suitable for input into PLABQTL. The data will be in the vector format. See the PLABQTL manual for more details.