Version 0.42

qtl2 0.42 (2026-06-08)

New features

• 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.

Minor changes

• Added a package logo.

Bug fixes

• In read_cross2() and read_pheno(), for phenotype covariates, convert columns to numeric if they look like numbers. (Issue #37)

• If input to find_peaks() had no column names, no peaks would be found. Added warning, plus a default set of column names.