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

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

Description

Convert a genotypes object to an R/qtl object

Usage

as.rqtl(gty, type = c("f2", "bc"), chroms = paste0("chr", c(1:19, "X")),
  ...)

Arguments

gty	a genotypes object
type	cross type for R/qtl (only "bc" [backcross] and "f2" [F2 intercross] currently supported)
chroms	vector of chromosome names to include in output (in order)
...	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, so only markers with non-zero, non-missing genetic positions will be included in the output of this function.

Value

an object of class cross, with the specified cross type

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.genotypes.cross (for inverse operation)

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