alignCross: Graphical linkage group identity and alignment.

In ASMap: Linkage Map Construction using the MSTmap Algorithm

Graphical linkage group identity and alignment.

Description

A graphical tool for identity and alignment of linkage groups in qtl cross objects using reference maps.

Usage

alignCross(object, chr, maps, ...)

Arguments

object	A qtl cross object with any class structure.
chr	A character string of linkage group names or a logical vector equal to the length of the number of linkage groups (see subset.cross).
maps	A named list of qtl cross objects or data.frame objects containing markers that are present in object. The matching markers are used to identify and orient the object linkage groups (see Details).
...	Other arguments to be passed to the high level lattice plot.

Details

If any list elements of map are qtl "cross" objects then marker names, linkage group identity and genetic distance information are extracted. List elements of map that are data.frame objects must explicitly contain named columns "marker", "ref.chr", "ref.dist" otherwise an error will be produced.

For each linkage group determined by chr, the contents of the listed maps are checked for matching markers in object. For each chr and reference map combination, a scatter plot of the object genetic distances against the reference distances is displayed with reference linkage group names as the plotting character. If a linkage group is in correct orientation the overall slope of the scatter plot should be positive. If a linkage group requires inverting then the overall slope should be negative.

Value

A lattice panel plot is displayed with panels labelled by a combination of chr and the maps used as a reference. A data frame of these results is also invisibly returned.

Author(s)

Julian Taylor

References

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.

See Also

est.map

Examples

data(mapDH, package = "ASMap")

chrl <- sample(c(TRUE,FALSE), 23, replace = TRUE)
mapDH1 <- subset(mapDH, chr = chrl)
alignCross(mapDH, maps = list(DH = mapDH1), layout = c(3,5), col = 1:7)

ASMap documentation built on Nov. 1, 2024, 9:08 a.m.