NEWS.md

In rqtl/qtl2scan: Genome Scans for QTL Experiments

qtl2scan 0.5-25 (2017-11-16)

New features

• Added scan1snps() to do single-QTL scan at SNPs imputed from founder genotypes; can be used to scan the full genome or a defined region.

• Added arguments lodcolumn and chr to top_snps() so that it can deal with multiple LOD score columns and/or multiple chromosomes.

qtl2scan 0.5-24 (2017-11-06)

Minor changes

• Improve handling of missing names in interp_map(), and ensure that when markers are on top of each other in the oldmap, their positions in the newmap don't get changed.

qtl2scan 0.5-23 (2017-10-17)

Minor changes

• Turn off debug C++ code

Bug fixes

• Fix bug in est_herit() regarding dependent covariate columns when missing values in the phenotypes. Need to call drop_depcols() again after having omitted individuals with missing phenotypes.

qtl2scan 0.5-20 (2017-08-09)

New features

• Removed the preserve_intercept argument from scan1blup(). The default (FALSE), adding the intercept to the BLUPs, no longer makes sense to me. (Better to have an option in scan1coef() to get estimated genetic effects that sum to 0; which we'll add in the future.)

Minor changes

• Check for linearly dependent columns in covariate matrices after omitting individuals.

• Check for +/- Inf in the phenotypes and covariates, rather than just NAs.

• In linear regression routines, and checks that inputs are appropriately sized.

qtl2scan 0.5-18 (2017-07-09)

Bug fixes

• Fix bug that prevented scan1() from being used with a decomposed kinship matrix.

• For the example contrasts in scan1coef, scan1blup, and fit1, the contrasts for the additive effect in an intercross should be (-1,0,1) not (-0.5,0,0.5). Also fixed in the user guide.

• In subset_kinship, if subsetting a decomposed kinship matrix by individual, check whether perhaps it's not actually being changed in which case just ignore the ind argument.

qtl2scan 0.5-14 (2017-06-05)

Minor changes

• Revised installation instructions.

• Small changes to user guide regarding use of library(qtl2).

qtl2scan 0.5-13 (2017-05-03)

Bug fixes

• Fixed linreg_eigen.cpp and matrix.cpp to work with RcppEigen 0.3.3.3.0.

qtl2scan 0.5-12 (2017-04-29)

New features

• Implemented model="binary" (for phenotypes with values 0/1) in scan1, scan1coef, scan1perm, and fit1. (Not available with kinship correction.)

Bug fixes

• Give a better error message if phenotypes (or covariates) are missing rownames (or, with a vector, names)

qtl2scan 0.5-11 (2017-04-28)

Minor fixes

• Reduce repeated code dealing with kinship matrices.

Bug fixes

• Fix bug regarding treatment of pre-decomposed kinship matrix in scan1.

• decomp_kinship crashes R if input has dimension 0x0; halt with an error in this case.

qtl2scan 0.5-9 (2017-04-19)

Minor changes

• Revised subset_scan1 (and the internal function subset_kinship) to use the same options for subsetting by chromosome as the functions in R/qtl2geno, most importantly use of "negative" chromosome indexes, like "-X".

qtl2scan 0.5-8 (2017-04-03)

New features

• Added fit1() to fit a single-QTL model at a single fixed position and return the LOD score, estimated coefficients, individual contributions to the LOD score, and (if se=TRUE) standard errors.

• In scan1coef() and scan1blup(), added an argument nullcovar for covariates to include only under the null hypothesis (of no QTL). This is only used in the case that kinship is provided but hsq is not, as these may be needed for the X chromosome to get the estimated residual heritability.

qtl2scan 0.5-7 (2017-03-21)

New features

• Added dim.calc_genoprob and dimnames.calcgenoprob, 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)).

qtl2scan 0.5-6 (2017-03-17)

New features

• Added scan1perm to perform a permutation test to establish genome-wide significance in a single-QTL genome scan by scan1.

• Also added functions rbind.scan1perm and cbind.scan1perm for combining scan1perm results, and summary.scan1perm to obtain significance thresholds.

Bug fixes

• Fixed a bug in scan1. This would only show up if you were using a kinship matrix and scanning the X chromosome on its own with special X chr covariates (Xcovar). (Accidentally was acting as if it were an autosome and so ignoring Xcovar.)

qtl2scan 0.5-5 (2017-03-13)

New features

• Refactored to simplify the main data structures for scan1, scan1coef, and scan1blup output, and to deal with the refactoring of data structures in qtl2geno. Functions like max_scan1, find_peaks, lod_int, and bayes_int now need you to provide a map. Similarly, to subset scan1 results by chromosome, you need to provide a map to the subsetting function.

• Pulled the "snpinfo" attribute out of the scan1 object. Now you need to use index_snps to identify groups of equivalent SNPs prior to running genoprob_to_snpprob. index_snps adds some new columns to the snpinfo data frame, which are then needed by top_snps.

rqtl/qtl2scan documentation built on May 28, 2019, 2:36 a.m.