R/qtl2 version 0.16

[Karl Broman]

We've released a new version of R/qtl2, version 0.16. 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")

karl

---

qtl2 0.16 (2018-07-23)

New features

• Added pull_genoprobint() for pulling out the genotype probabilities for a given genomic interval. Useful, for example, to apply scan1blup() over a defined interval rather than an entire chromosome.

• scan1(), scan1perm(), scan1coef(), fit1(), and scan1snps() can now use weights when kinship is provided, for example for the case of the analysis of recombinant inbred line (RIL) phenotype means with differing numbers of individuals per line. The residual variance matrix is like $v[h^2 K + (1-h^2)D]$ where D is diagonal {1/w} for weights w.

• Added weights argument to est_herit().

• Added add_threshold() for adding significance thresholds to a genome scan plot.

• Added predict_snpgeno() for predicting SNP genotypes in a multiparent populations, from inferred genotypes plus the founder strains' SNP alleles.

• In genoprob_to_snpprob(), the snpinfo argument can now be a cross object (for a multiparent population with founder genotypes), in which case the SNP information for all SNPs with complete founder genotype data is calculated and used.

• max_scan1() with lodcolumn=NULL returns the maximum for all lod score columns. If map is included, the return value is in the form returned by find_peaks(), namely with lodindex and lodcolumn arguments added at the beginning.

• Added replace_ids() for replacing individual IDs in an object. S3 method for "cross2" objects and output of calc_genoprob(), viterbi(), maxmarg(), and sim_geno().

• Added clean_scan1() plus generic function clean() that works with both this and with clean_genoprob(). clean_scan1() replaces negative values with NA and removes rows that have all NAs.

Minor changes

• More informative error message in est_herit(), scan1(), etc., when covariates and other data are not numeric.

• Fixed pull_genoprobpos() so it will work with qtl2feather (and qtl2fst).

• In plot_genes(), if xlim is provided as an argument, subset the genes to those that will actually appear in the plotting region.

• Revise find_marker() so that the input map can also be a "snp info" table (with columns "snp_id", "chr" and "pos").

• Added find_index_snp() for identifying the index SNP that corresponds to a particular SNP in a snp info table that's been indexed with index_snps().

• Add overwrite argument (default FALSE) to zip_datafiles(), similar to that for write_control_file().

• plot_snpasso() now takes an argument chr.

• max_scan1() no longer gives a warning if map is not provided.

• insert_pseudomarkers() will now accept pseudomarker_map that includes only a portion of the chromosomes.

• In fit1(), replaced tol and maxit and added ... which takes these plus a few additional hidden control parameters.

Bug fixes

• Fix a bug in index_snps(); messed up results when start and end outside the range of the map.

• Fix a bug in scan1snps() regarding use of chr argument: need to force to be unique character strings, and avoid unnecessary warning about start and end.

• Fix a bug in scan1snps() where it didn't check that the genoprobs and map conform.

• Revised underlying binary trait regression function to avoid some of the tendency towards NAs.