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Filenaming Conventions

The QTL Cartographer system reads and creates many files and each has a default name. For example, the default output file for Rmap is We find it convenient to specify a filename stem and allow for the filename extension to indicate which program created it, and what it contains. Suppose we were working on a corn data set. We might use ``corn'' as the filename stem. Then Rmap would write its output to and its error messages to corn.log. Rqtl would write its output to corn.qtl, etc. Table 1.5 summarizes the standard file name extensions in the QTL Cartographer system. Beginning with version 1.12, the default behavior of QTL Cartographer is to use a filename stem: If none is given, then ``qtlcart'' will be the stem. Unless specifically written in the qtlcart.rc file, the old default names of Rmap.out, Rqtl.out, etc., will no longer be used. These old default names will be used as filetype identifiers. In the output files, there will be a token ``-filetype'' followed by a token from the fourth column of Tables 1.5-1.6. Note that Zmapqtl creates some interim files, and that Preplot will create many other files in addition to the Gnuplot control file: See Section 4.2 for details. The ``-filetype'' specifier will greatly aid programs such as Rmap and Rcross in translating files. As QTL Cartographer develops, this feature will be used more extensively. Once the stem is set in the menu, it will be remembered as long as a resource file is present.

Table 1.5: Standard Filename Extensions and File types for Output Files
Program Extension Contents -filetype
Rmap .map genetic linkage map Rmap.out
Rqtl .qtl QTL model Rqtl.out
Rcross .cro data file (markers, traits) Rcross.out
Qstats .qst QstatsAnalysis Qstats.out
LRmapqtl .lr Single Marker Analysis LRmapqtl.out
SRmapqtl .sr Stepwise Regression Analysis SRmapqtl.out
Zmapqtl .z IM-CIM Results Zmapqtl.out
JZmapqtl .z# Multitrait Results JZmapqtl.out
Prune .mpb pruned genetic linkage map Rmap.out
Prune .crb pruned data file Rcross.out
Preplot .plt Gnuplot Control file Preplot.plt
Eqtl .eqt Summary of Zmapqtl Results Eqtl.out
MImapqtl .mim MImapqtl results MImapqtl.out

In the interactive menu, if you pick an item to change (say a filename), you can wipe it out by inputting a solitary period. This way, if you had specified an input file in an earlier run, you can delete it.

Table 1.6: Miscellaneous Files and File types
Program Example Contents -filetype
Rmap qtlcartm.inp genetic linkage map map.inp
Rmap qtlcart.maps Mapmaker/EXP output mapmaker.maps
Rqtl qtlcartq.inp genetic model file qtls.inp
Rcross qtlcartc.inp data file (markers, traits) cross.inp
Rcross qtlcart.raw Mapmaker/EXP input mapmaker.raw
Zmapqtl qtlcart.z3c Perm. test interim file ZipermC.out
Zmapqtl qtlcart.z3e Perm. test interim file ZipermE.out
Zmapqtl qtlcart.z3a Bootstrap interim file Ziboot.out
Eqtl qtlcart.z3b Bootstrap summary file Ziboots.out
Zmapqtl qtlcart.z3i Jackknife interim file Zijack.out
MImapqtl qtlcart.res Residuals dataset file Rcross.out
MImapqtl qtlcart.mqt Model output file Rqtl.out
Eqtl qtlcart.z3j Jackknife summary file Zijacks.out

In addition to the files specified in the table, we assume that files with extensions ``maps'' and ``raw'' are Mapmaker/EXP genetic linkage map and raw data files, respectively. These and other files recognized by QTL Cartographer are listed in Table 1.6.

next up previous contents index
Next: Simulating/Reformatting Data Up: General Usage of the Previous: A General Test   Contents   Index
Christopher Basten 2002-03-27