An R package with tools for analyzing QTL experiments.
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To participate in discussion about the use of R/qtl, join the Google group, R/qtl discussion
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To participate in discussion about the use of R/qtl2, join the Google group, R/qtl2 discussion
R/qtlcharts and d3panels
Various examples of D3-based interactive graphs.
Various R functions that I find useful, assembled into an R package.
R package for searching arXiv (an archive of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics). The package is part of the rOpenSci project.
R packages for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data on two tissues. R/lineup is closely tied to the R/qtl package. R/lineup2 is a redesign to be more general.
An R package for the analysis of crossover interference in experimental crosses, particularly regarding the gamma model.
An R package for the fit of a simple linear mixed model useful for genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping.
An R package for calculation of two- and three-locus probabilities in multiple-strain recombinant inbred lines, and the simulation of such lines. See the related paper: Broman KW (2005) The genomes of recombinant inbred lines. Genetics 169:1133-1146
An R package for evaluating whether a microbiome sample is the mixture of two source samples. We are thinking of shotgun sequencing data on the microbiome sample plus dense SNP genotype data on the two potential source samples. We assume that the data has been reduced to a three-dimensional array of read counts: the 3 possible SNP genotypes for the first sample × the 3 possible SNP genotypes of the second sample × the 2 possible SNP alleles on the reads. We then fit a model with contaminant probability p = proportion of the microbiome sample coming from the second sample and e = rate of sequencing errors. See the related preprint.
An R package for the inference of full sibling families with data on dominant genetic markers (such as RAPDs), following the hierarchicical clustering approach of Apostol et al. (1993) Theor Appl Genet 86:991-1000. The title follows from Fortran software written by WC Black IV.
Software for estimating the odds ratio for siblings for a binary phenotype, adjusting for covariates, using generalized estimating equations.
Software for testing, by computer simulation, various approaches to mapping QTLs in a backcross experiment. This was written for the manuscript Broman and Speed (2002) A model selection approach for the identication of quantitative trait loci in experimental crosses. J Roy Stat Soc B 64:641-656. Also see the R/qtl package.
Version 0.67 (24 August 2000) Software for verifying relationships between all pairs of individuals in a linkage study, using the approach of Boehnke and Cox (Am J Hum Genet, 61:423-429, 1997), with the modification described by Broman and Weber (Am J Hum Genet 63:1563-1564, 1998), to allow for the presence of genotyping errors. We look only at the relationships MZ twins, parent/offspring, fullsibs, halfsibs and unrelated.
Note: I am no longer actively developing this software. You may wish to check out Mary Sara McPeek and Lei Sun’s program PREST. It has a similar aim, and calculates a more extensive set of statistics, includes measures of statistical significance, and also looks at avuncular and first cousin relationships. Other alternatives include the programs Borel, Relpair, Relative, Reltype and Siberror. Go to the Rockefeller software list to find these programs.
The input/output for my program is rather crude. If you use the software, please reference the above papers in any publications.
A perl script for converting data from linkage format to that used by RelCheck is included with the software.
Version 0.50 (7 Feb 2000)
Software for QTL analysis of an F2 intercross experiment, including forward selection for multiple QTLs, all pairs of loci, and pairwise interactions.
Note: This is very preliminary, the input and output are not well documented, and I’m no longer actively developing this software. Look at R/qtl, instead.