as.genotypes: Convert an 'R/qtl' object to a 'genotypes' object

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Convert an R/qtl object to a genotypes object

Usage

as.genotypes(x, ...)

Arguments

x	a qtl::cross object
...	ignored

Details

Karl Broman's R/qtl is a widely-used package for mapping quantiative traits in experimental crosses of laboratory organisms and crop plants. It expects genotypes to be coded with respect to parental lines: eg. AA, AB, BB for an F2 cross between (true-breeding) lines A and B. Be sure to recode genotypes in that mannyer way before passing them to this function.

Marker positions in R/qtl are expressed in centimorgans, not basepairs. On conversion, physical positions are faked by assuming recombination rate 1 cM per 1 Mbp and rounding to the next-lowest integer.

Only crosses of type "f2" (F2 intercross) or "bc" are supported, and partially- informative genotypes will probably be mangled.

Value

an object of class genotypes

References

R/qtl: http://www.rqtl.org

Broman KW, Wu H, Sen S, Churchill GA. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890. doi:10.1093/bioinformatics/btg112.

Broman KW, Sen S. (2009) A Guide to QTL Mapping with R/qtl. Springer, New York.

See Also

read.cross, as.rqtl.genotypes (for inverse operation)

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.