R/qtl2 version 0.22

[Karl Broman]

We've released a new version of R/qtl2. Install the update with

    update.packages(ask=FALSE, repos="https://rqtl.org/qtl2cran")

Or install from scratch with

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

The changes are shown below. R/qtl2fst and R/qtl2convert have also been updated.

karl

---

Major changes

• Added some functions for diagnostics: recode_snps(),
  calc_raw_het(), calc_raw_geno_freq(), calc_raw_maf(), and
  calc_raw_founder_maf().

• Added argument blup to fit1(), for getting BLUPs for a single
  fixed QTL position. At present, just gives estimates and
  coefficients by calling scan1blup() with a single position.

• pull_genoprobpos() can now take either a marker name (as before) or
  a set of map, chromosome, and position (from which it uses
  find_marker() to get the marker name).

• Added plot function for the results of compare_geno(). (Plots
  histogram of upper triangle.)

• Added functions n_founders() and founders() for getting the
  number of founders and the founder strain names for a cross2 object.

• scan1() now takes an optional hsq argument, so that the residual
  heritability may be specified rather than estimated.

Minor changes

• write_control_file() now allows cross info codes with a cross info
  file (previously only allowed with a covariate). read_cross2()
  gives a warning if there are cross info conversion codes but more
  than one cross info column.

• Small fix in read_cross2() to allow multiple cross info covariates.

• Added a check that the founder genotypes have the same strain IDs on
  each chromosome.

• convert2cross2() now includes alleles component even if it
  wasn't present as an attribute.

• Added function sdp2char() for converting numeric SDP codes to
  character strings like "ABC|DEFGH".

• Updated mouse gene database with 2019-08-12 data from
  MGI.

• get_common_ids() strips off names from output, just in case.

• Added internal functions rqtl1_crosstype() and rqtl1_chrtype().

Bug fixes

• Fixed typo in help for scan1() and related functions.

• genoprob_to_snpprob() was giving an error if you gave a cross2
  object in place of a snpinfo table and it had monomorphic markers.

• Fixed problem with weights in scan1() and related functions when
  their derived from table(). Make sure they're a plain numeric
  vector, not an array.

• Fixed check_cross2(): the check for invalid genotypes wasn't
  happening.

• Better error message for the case that there are no markers in
  common between map and genotypes.

• extract_dim_from_header(), used by read_cross2() and read_csv(),
  now just looks for the number part in the rest of the line.

• maxlod() now handles missing values (forcing na.rm=TRUE). If all
  values are missing it gives a warning and returns -Inf.
  [Fixes Issue #134.]

• In max_scan1(), treat the case that the input has no column names.
  [Fixes Issue #133.]

• max_scan1() was giving a messed up error message if lodcolumn
  was out of range. [Fixes Issue #132.]

• Revised the script inst/scripts/create_ccvariants.R to capture all
  of the consequences and genes for each SNP (rather than just the
  first), and fixing a bug that prevented capture of indels from
  chromosomes 6-X. Consequently, revised the example SQLite database
  extdata/cc_variants_small.sqlite and associated tests.