R/qtl2 version 0.18

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Karl Broman

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Feb 8, 2019, 9:19:56 AM2/8/19
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I've released a new version of R/qtl2, version 0.18. Changes are listed below.

To upgrade:

    update.packages(repos="http://rqtl.org/qtl2cran")

Or do a fresh install:

    install.packages("qtl2", repos="http://rqtl.org/qtl2cran")

Also, the R/qtl2 paper is now published in Genetics. If you use R/qtl2, please cite:

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2019) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. Genetics 211:495-502 https://doi.org/10.1534/genetics.118.301595

karl

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qtl2 0.18 (2019-02-08)

New features

  • Added plot_lodpeaks() for scatterplot of LOD score vs position for inferred QTL from find_peaks() output.

  • Added new cross types "genril" and "genail", implemented to handle any number of founders; include the number of founders in the cross type, for example "genril38" or "genail38". The cross information has length 1 + number of founders, with first column being the number of generations and the remaining columns being non-negative integers that indicate the relative frequencies of the founders in the initial population (these will be scaled to sum to 1). "genril" assumes the progeny are inbred lines (recombinant inbred lines, RIL), while "genail" assumes the progeny have two random chromosomes (advanced intercross lines, AIL).

  • The internal function batch_vec() now made user-accessible, and takes an additional argument n_cores. This splits a vector into batches for use in parallel calculations.

  • The internal function cbind_expand() now made user-accessible. It's for combining matrices using row names to align the rows and expanding with missing values if there are rows in some matrices but not others.

  • In plot_peaks(), added lod_labels argument. If TRUE, include LOD scores as text labels in the figure.

  • Added function calc_het() for calculating estimated heterozygosities, by individual or by marker, from genotype probabilities derived by calc_genoprob().

Minor changes

  • Small corrections to documentation.

  • Revise some tests due to change in Recla and DOex datasets at https://github.com/rqtl/qtl2data

  • Add tests of decomposed kinship matrix (from decomp_kinship()) with scan1().

  • rbind_scan1() and cbind_scan1() no longer give error if inputs don't all have matching attributes.

  • Change default gap between chromosomes in plot_scan1() (and related) to be 1% of the total genome length.

Bug fixes

  • Fixed bug in subset_kinship() that prevented scan1() from working with decomposed "loco" kinship matrices.

  • Fixed descriptions in help files for cbind.calc_genoprob() and rbind.calc_genoprob(), for column- and row-binding genotype probabilities objects (as output by calc_genoprob(). cbind() is for the same set of individuals but different chromosomes. rbind() is for the same set of markers and genotypes but different individuals. Made similar corrections for the related functions for sim_geno() and viterbi() output.

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