R/qtl2 version 0.42
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Karl Broman
Jun 8, 2026, 11:27:08 PM (9 days ago) Jun 8
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A new version of R/qtl2 (version 0.42) has been released on CRAN. Windows and Mac binaries will be available within a few days.
There are a lot of additions in this revision; the new features are outlined below.
Karl Broman
---
- fit1() can return the full variance-covariance matrix of the coefficients, with the argument var=TRUE. In this case, the se argument is ignored, but the standard errors are also included. The SEs for the case zerosum=TRUE have been corrected.
- Added function plot_cistrans() for plotting the results of eQTL or pQTL analyses, with gene location on the y-axis and QTL location on the x-axis.
- Added function calc_hotspots() for counting QTL in a sliding window, to identify QTL hotspots, for example in eQTL/pQTL experiments.
- Added function plot_scan1_heatmap() for plotting scan1 results for multiple traits as a heat map. Also added a function plot_colorscale() for plotting a corresponding color scale.
- Added function plot_geno() for plotting genome-wide genotypes for multiple individuals.
- Added functions for manipulating the "phased genotypes" output of guess_phase(): subset.phasedgeno(), rbind.phasedgeno(), and cbind.phasedgeno().
- Added arguments add and offset to plot_ci(), so that you can add additional sets of confidence intervals, shifted relative to each other, to a plot.
There are a lot of additions in this revision; the new features are outlined below.
Karl Broman
---
- fit1() can return the full variance-covariance matrix of the coefficients, with the argument var=TRUE. In this case, the se argument is ignored, but the standard errors are also included. The SEs for the case zerosum=TRUE have been corrected.
- Added function plot_cistrans() for plotting the results of eQTL or pQTL analyses, with gene location on the y-axis and QTL location on the x-axis.
- Added function calc_hotspots() for counting QTL in a sliding window, to identify QTL hotspots, for example in eQTL/pQTL experiments.
- Added function plot_scan1_heatmap() for plotting scan1 results for multiple traits as a heat map. Also added a function plot_colorscale() for plotting a corresponding color scale.
- Added function plot_geno() for plotting genome-wide genotypes for multiple individuals.
- Added functions for manipulating the "phased genotypes" output of guess_phase(): subset.phasedgeno(), rbind.phasedgeno(), and cbind.phasedgeno().
- Added arguments add and offset to plot_ci(), so that you can add additional sets of confidence intervals, shifted relative to each other, to a plot.
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