polymapR (version 1.1.7)

check_map: Check the quality of a linkage map

Description

Perform a series of checks on a linkage map and visualise the results using heatplots. The difference between the pairwise and multi-point r estimates are also plotted against the LOD of the pairwise estimate. The weighted root mean square error of these differences (weighted by the LOD scores) is printed on the console.

Usage

check_map(
  linkage_list,
  maplist,
  mapfn = "haldane",
  lod.thresh = 5,
  detail = 1,
  plottype = c("", "pdf", "png")[1],
  prefix = ""
)

Arguments

linkage_list

A named list with r and LOD of markers within linkage groups.

maplist

A list of maps. In the first column marker names and in the second their position.

mapfn

The map function used in generating the maps, either one of "haldane" or "kosambi". By default "haldane" is assumed.

lod.thresh

Numeric. Threshold for the LOD values to be displayed in heatmap, by default 5 (set at 0 to display all values)

detail

Level of detail for heatmaps, by default 1 cM. Values less than 0.5 cM can have serious performance implications.

plottype

Option to specify graphical device for plotting, (either png or pdf), or by default "", in which case plots are directly plotted within R

prefix

Optional prefix appended to plot names if outputting plots.

Examples

if (FALSE) {
data("maplist_P1","all_linkages_list_P1")
check_map(linkage_list = all_linkages_list_P1, maplist = maplist_P1)
}