cross2_to_grcm39 {mmconvert}

Convert a cross2 object to use mouse build GRCm39

Description

Convert a cross2 object (with genotypes from one of the MUGA arrays) to use mouse build GRCm39 and the revised Cox map positions, revising marker order and omitting markers that are not found.

Usage

cross2_to_grcm39(cross, array = c("guess", "gm", "mm", "mini", "muga"))

Arguments

cross

Object of class "cross2", as produced by qtl2::read_cross2(). Must have markers from just one of the MUGA arrays.

array

Character string indicating which of the MUGA arrays was used ("gm" for GigaMUGA, "mm" for MegaMUGA, "mini" for MiniMUGA, or "muga" for the original MUGA), or "guess" (the default) to pick the array with the most matching marker names.

Value

The input cross object with markers subset to those in build GRCm39 and with pmap and gmap replaced with the GRCm39 physical map and revised Cox genetic map, respectively.

See Also

MUGAmaps

Examples

library(qtl2)
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)
DOex_rev <- cross2_to_grcm39(DOex)