NEWS.md

In rqtl/qtl2geno: Treatment of Marker Genotypes for QTL Experiments

qtl2geno 0.5-38 (2017-11-20)

New features

• Added interp_genoprob() for linear interpolation of genotype probabilities, useful when comparing two sets of genotype probabilities derived by different methods and calculated at slightly different positions.

qtl2geno 0.5-37 (2017-11-09)

Minor changes

• Have zip_datafiles() give a warning if any of the paths include "..".

• insert_pseudomarkers() now has a cores argument for doing calculations in parallel on multiple CPUs.

qtl2geno 0.5-36 (2017-11-09)

New features

• Added compare_genoprob() for getting tabular comparison of two sets of genotype probabilities, for a single individual on a single chromosome.

qtl2geno 0.5-33 (2017-10-04)

Minor changes

• Added deterministic argument to guess_phase().

qtl2geno 0.5-30 (2017-08-11)

Minor changes

• Turned off debug C++ code.

qtl2geno 0.5-29 (2017-08-04)

Minor changes

• Added additional tests of check_cross2()

Bug fixes

• For crosstype "ail3", forgot to include the functions for requiring and checking the founder genotypes.

• check_cross2 wasn't checking for missing names in gmap, pmap, and founder_geno

qtl2geno 0.5-28 (2017-07-31)

New features

• Added function guess_phase(), for guessing the phase of imputed genotypes (such as from maxmarg()), mostly for visualization of genotypes of one individual from a multi-parent population.

Bug fixes

• Fix handling of missing values in internal functions mpp_decode_geno() and mpp_encode_alleles().

qtl2geno 0.5-26 (2017-06-29)

New features

• Implemented two new crosstypes: "dh6" for 6-way doubled haploids (for a set of maize MAGIC populations developed at the Wisconsin Crop Innovation Center) and ail3 for 3-way advanced intercross lines.

Minor changes

• Added internal C++ function check_founder_geno_size() for checking the dimensions of the founder genotype data from R, and added this check to the check_cross2() function.

qtl2geno 0.5-25 (2017-06-29)

New features

• Added function read_csv_numer() that is like read_csv() but assumes that all columns expect the first are strictly numeric. Now used by read_pheno() to vastly speed things up (because otherwise I was assuming everything was character and then converting, and that conversion to numeric was deathly slow).

qtl2geno 0.5-24 (2017-06-12)

Bug fixes

• Fix formatting problem in output of summary.cross2() within RStudio.

qtl2geno 0.5-23 (2017-06-05)

Minor changes

• Revised installation instructions.

qtl2geno 0.5-22 (2017-05-24)

New features

• Added function scale_kinship() which converts a kinship matrix (or a list of such, in the case of the "leave one chromosome out" method) to be like a correlation matrix.

• Removed the "normalize" argument from calc_kinship(), though left the internal function normalize_kinship() in place, for now.

Minor changes

• insert_pseudomarkers now gives an error if the input map is NULL.

qtl2geno 0.5-21 (2017-05-10)

New features

• count_xo now works with the output of sim_geno. The result is a 3d-array of counts of crossovers for each individual on each chromosome in each imputation.

qtl2geno 0.5-20 (2017-05-04)

New features

• Added chisq_colpairs which performs chi-square tests for independence on all pairs of columns of a matrix. It just calculates the statistics.

qtl2geno 0.5-19 (2017-05-01)

Minor changes

• Added an argument save_rf to est_map(); if TRUE, the estimated recombinations are saved as an attribute ("rf") of the result. This can be useful for diagnostic purposes, for example when the estimated recombination fraction between markers is > 1/2. (After converting to genetic distance, rf>1/2 is indistinguishable from rf=1/2.)

qtl2geno 0.5-18 (2017-04-19)

New features

• New function reduce_map_gaps that reduces the length of any gaps in map. (Gaps greater than min_gap are reduced to min_gap.)

• maxmarg now picks at random among genotypes that jointly share the maximum probability. Previously, it picked the first among these. Added an argument tol; if two genotypes have probabilities that differ by no more than tol, they are treated as having the same probability.

• New function calc_entropy takes the results of calc_genoprob and calculates, for each individual at each genomic postion, the entropy of the genotype probability distribution, as a measure of missing information.

Bug fixes

• Fix bug in find_map_gaps regarding the case that the output are empty.

• Fix bug in attempting to subsett calc_genoprob output by individual using individuals that aren't present in the data.

• Fix bug in est_map where it was producing NaNs in some cases.

qtl2geno 0.5-17 (2017-04-17)

Bug fixes

• read_cross2 now unzips a .zip file to a separate directory, to avoid possibility of clashing of multiple sets of files.

• read_cross2 will now ignore any JSON or YAML files in the .zip file that have the pattern __MACOSX/._*.

• read_cross2 will stop with an error if a .zip file contains multiple JSON or multiple YAML files. If there's both a YAML and a JSON file, the YAML file is used and a warning is issued.

Minor changes

• est_map now gives a warning if it reaches the maximum number of iterations without converging.

qtl2geno 0.5-16 (2017-04-16)

New features

• Implemented new cross types "risib4", "risib8", and "magic19". The "risib8" cross type corresponds to the Collaborative Cross. The "magic19" cross type corresponds to the 19-way Arabidopsis MAGIC lines of Kover et al (2009) PLOS Genetics 5:e1000551.

qtl2geno 0.5-15 (2017-04-14)

New features

• Added argument lowmem to est_map; default is FALSE, which corresponds to a new implementation that uses more memory but is considerably faster.

• Added function find_map_gaps for identifying larger inter-marker gaps in a genetic map.

• Added function calc_geno_freq for calculating genotype frequencies, by individual or by marker (from the multipoint genotype probabilities returned by calc_genoprob).

qtl2geno 0.5-14 (2017-04-05)

New features

• Implemented new cross types "riself4", "riself8", and "riself16", for multi-way MAGIC populations (multi-way RILs by selfing).

Bug fixes

• Fixed problem in read_cross2 in the case that data has a physical map but not a genetic map.

Minor changes

• Added argument 'overwrite' to write_control_file; if TRUE, overwrite the file, if it's present. (Previously, you were always forced to first remove it.)

qtl2geno 0.5-13 (2017-04-03)

New features

• Added function ind_ids_covar to grab individual IDs from the covariate data.

• ind_ids() now return individuals that are in any of geno, pheno, covar.

Bug fixes

• subset_cross2() now deals properly with the case that chromosome or individual IDs are not found in cross object, and deals with the case that geno and pheno (and covar) have different individuals.

qtl2geno 0.5-12 (2017-03-30)

New features

• Added functions count_xo and locate_xo for getting estimates of the number of crossovers on each chromosome in each individual, and of their locations.

• Added compare_geno for comparing raw genotypes between pairs of individuals (to look for possible sample duplicates).

• Added calc_errorlod to help identify potential genotyping errors (and problem markers or individuals).

qtl2geno 0.5-9 (2017-03-23)

Minor changes

• Made various small improvements to the handling of problems in the input files.

• Small changes to better handle genotype probabilities that are in the qtl2feather format.

qtl2geno 0.5-8 (2017-03-21)

New features

• Added internal functions dim.calc_genoprob and dimnames.calc_genoprob, from Brian Yandell, for use with qtl2feather, which uses feather to store genotype probabilities in a file (to save memory).

• In precess of revising various functions to use qtl2feather, particularly in grabbing dimnames (with the above functions), but also to avoid seq(along=genoprobs) and instead use seq_len(length(genoprobs)).

qtl2geno 0.5-7 (2017-03-21)

New features

• Removed the distinction between "lines" and "individuals", and the linemap component in the input that connected them. (While for RILs like the Collaborative Cross, we may want to work with individual-level phenotypes, it seems best to deal with that outside of the cross object.)

• Removed the functions n_lines() and line_ids(). Added some functions:

  • n_ind_geno() for number of genotyped individuals, and ind_ids_geno() to get their IDs.
  • n_ind_pheno() for number of phenotyped individuals, and ind_ids_pheno() to get their IDs.
  • n_ind_gnp() for number of individuals with both genotypes and phenotypes, and ind_ids_gnp() to get their IDs.

• Also, n_ind() and ind_ids() now return the total number of individuals, across both genotypes and phenotypes.

qtl2geno 0.5-6 (2017-03-17)

New features

• Added a function find_ibd_segments that takes genotypes for a set of inbred strains and searches for segments where strain pairs look to be IBD.

qtl2geno 0.5-5 (2017-03-13)

New features

• Refactored to simplify the main data structures for genetic map and genotype probabilities. calc_genoprob now needs you to provide a pseudomarker map (created with insert_pseudomarkers).

rqtl/qtl2geno documentation built on May 28, 2019, 2:36 a.m.