splitChr: Split markers into chromosomes

In grafab/pergola: Toolbox for Polyploid Genetic Data

Description

This function splits markers into linkage groups (LG), which ideally represent chromosomes. The split is based on hierarchical clustering with a single linkage distance.

Usage

splitChr(rf, height = 0.4, nchr = NULL, method = "single",
  filter = FALSE, thresh = 0.05, rm.dup = TRUE)

Arguments

rf	Matrix of pairwise recombination frequencies.
height	Threshold value for grouping the markers.
nchr	Expected number of chromosomes.
method	Default is "single", which is used for the hierarchical clustering.
filter	Logical, if the result should be filtered or not. Default is FALSE. Creates zeros for the markers below the threshold.
thresh	Threshold for filtering. Default is 0.05, i.e. linkage groups with less than 5% of markers, are filtered out.
rm.dup	Logical, if the duplicated markers should be filtered out. TRUE is highly recommended because the markers have no added value for the linkage map.

Value

Vector of cluster relationship. Same length and order as the matrix of recombination frequencies.

Examples

data(simTetra)
simTetrageno <- basesToGenotypes(simTetra, 4)
rfMat <- calcRec(simTetrageno, 4)
splitChr(rfMat, nchr = 7)

grafab/pergola documentation built on May 17, 2019, 8:18 a.m.