A Guide to QTL Mapping with R/qtl by Karl W. Broman

By Karl W. Broman

Quantitative trait locus (QTL) mapping is used to find the genetic and molecular structure underlying complicated quantitative characteristics. It has vital purposes in agricultural, evolutionary, and biomedical study. R/qtl is an extensible, interactive surroundings for QTL mapping in experimental crosses. it's applied as a package deal for the generally used open resource statistical software program R and incorporates a various array of QTL mapping tools, diagnostic instruments for making sure top of the range info, and amenities for the healthy and exploration of multiple-QTL versions, together with QTL x QTL and QTL x surroundings interactions. This e-book is a accomplished advisor to the perform of QTL mapping and using R/qtl, together with research layout, facts import and simulation, facts diagnostics, period mapping and generalizations, two-dimensional genome scans, and the honor of advanced multiple-QTL versions. reasonably demanding case stories illustrate QTL research in its entirety.

The ebook alternates among QTL mapping idea and examples illustrating using R/qtl. beginner readers will locate designated motives of the $64000 statistical strategies and, throughout the huge software program illustrations, might be capable of practice those techniques of their personal examine. skilled readers will locate info at the underlying algorithms and the implementation of extensions to R/qtl. There are one hundred fifty figures, together with ninety in complete colour.

Karl W. Broman is Professor within the division of Biostatistics and clinical Informatics on the college of Wisconsin-Madison, and is the manager developer of R/qtl. Saunak Sen is affiliate Professor in place of dwelling within the division of Epidemiology and Biostatistics and the heart for Bioinformatics and Molecular Biostatistics on the collage of California, San Francisco.

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The epistasis pattern for the two QTL is as before, but the effects are different in the two sexes. We reuse the wh object, created above, that indicated the individuals who were homozygous at both QTL. 6 Internal data structure In this section, we describe the internal data structures used by R/qtl for cross and genetic map objects and the R syntax required to get access to the data. Other data structures (such as those produced by the scanone and scantwo functions) will be described in later chapters.

Names(hyper$geno) [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" [12] "12" "13" "14" "15" "16" "17" "18" "19" "X" "10" "11" > sapply(hyper$geno, class) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" 16 17 18 19 X "A" "A" "A" "A" "X" Each component of geno is itself a list with two components, data (containing the marker genotype data) and map (containing the positions of the markers, in cM). The genotype data are coded 1/2 for homozygotes and heterozygotes in a backcross, and 1/2/3/4/5 for the genotypes AA/AB/BB/not BB/not AA in an intercross.

As a result, the crossovers on a random meiotic product may be obtained by “thinning” the chiasmata independently with probability 1/2. ) In the Stahl model, chiasmata arise according to two independent mechanisms, one following a χ2 model and the other exhibiting no interference; the observed chiasma locations are the superposition of the two processes. There is one additional parameter, p, giving the proportion of chiasmata to come from the mechanism exhibiting no interference. cross. By default, m=0 (in which case p is irrelevant), indicating no crossover interference.

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