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.
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.