Translating Data

Similar to Rmap and Rqtl, Rcross can translate files in a pair of special formats. The first format is the input format for Mapmaker/QTL. These would be the Mapmaker/QTL ``*.raw'' files. Simply invoke Rcross and specify that the input file is one of these files. The parameters that are for simulations are then ignored. REMEMBER: The first two words of a Mapmaker/QTL raw file should be ``data type''. Older versions of Rcross cannot process comments at the beginning of a raw file. In fact, it depends on those first two words to recognize the file as a Mapmaker/QTL raw file. Beginning with version 1.12, comments will be allowed in the beginning of a ``mapmaker.raw'' file if you include the ``-filetype mapmaker.raw'' indicator within the first 100 lines of your file. It is usually best to put this on the first line. Rcross will recognize the command and translate the file appropriately. You might want to get into the habit of putting the ``-filetype'' token (with an appropriate identifier) in your input files, as it will become more important in future releases of QTL Cartographer. There are two other things to keep in mind when using Mapmaker/QTL files. The first is that marker and trait names are truncated to eight characters in the output: Versions of QTL Cartographer prior to 1.12 will be tripped up by this. Secondly, Mapmaker/EXP has been known to translate underscores ``_'' as minus signs ``-'' in its output, so you might want to avoid them.

Another format is one designed for the QTL Cartographer system. It is defined in the file cross.inp included with the distribution and outlined in Section 6.3.2. Finally, Rcross can read files in it's own output format (filetype ``Rcross.out'') for translation to ``mapmaker.raw'' or ``cross.inp'' filetype formats.

Rcross can also read data files formatted for PLABQTL [Utz and MelchingerUtz and Melchinger1996]. You need to specify the filetype on the first line of the PLABQTL input file. The two filetypes are plabqtl0.inp for matrix input and plabqtl1.inp for vector input. In addition, if you have data with raw measurements from different environments then you need to add the phrase -environments x at the end of the first line, where $x$ is the number of environments.