check_map: Check the quality of a linkage map using heatplots

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description

Perform a series of checks on a linkage map and visualise the results using heatplots. Also shows the discrepency between the pairwise and multi-point r estimates, plotted against the LOD of the pairwise estimate.

Usage

check_map(linkage_list, maplist, mapfn = "haldane", lod.thresh = 5)

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)

Examples

## Not run: 
data("maplist_P1","all_linkages_list_P1")
check_map(linkage_list = all_linkages_list_P1, maplist = maplist_P1)

## End(Not run)

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.