R/qtl version 1.42-7

[Karl Broman]

A new version of R/qtl (1.42-7) has been released at its website (http://www.rqtl.org) and will be on CRAN shortly.

The big change: I removed the functions plot.errorlod, plot.geno, plot.info, plot.missing, plot.pheno, plot.pxg, and plot.rf. Changes in the process of submitting packages to CRAN have made this necessary. Each of the packages has alternative names that have been used in the tutorials for some years:

  plot.errorlod  plotErrorlod

  plot.geno      plotGeno

  plot.info      plotInfo

  plot.missing   plotMissing

  plot.pheno     plotPheno

  plot.pxg       plotPXG

  plot.rf        plotRF

If you have old scripts that use the old function names, add the following code at the top:

   source("https://rqtl.org/dotfunc.R")

I also fixed some bugs in refineqtl() and stepwiseqtl() regarding model="binary" and the case of NA LOD scores.

Karl Broman