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Version 0.22
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@kbroman kbroman released this 22 May 04:15
0.22
890f9a4

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.

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