cash-plotLM: BC, FS and IC method: Plot linkage maps

In tpbilton/GUSMap: Genotyping Uncertainty with Sequencing Data and Linkage Mapping (GUSMap)

BC, FS and IC method: Plot linkage maps

Description

Method for plotting linkage maps in GUSMap

Usage

BCobj$plotLM(LG = NULL, fun="haldane", col="black")
FSobj$plotLM(LG = NULL, fun="haldane", col="black")
ICobj$plotLM(LG = NULL, fun="haldane", col="black")

Arguments

LG	An integer vector specifying the indices of the linkage groups for which their linkage maps are to be plotted.
fun	Character value giving the mapping function to use which is passed to mfun.
col	Vector of character values giving the colors of the linkage maps.

Details

Function displays linkage maps computed using the $computeMap function.

For a list of mapping functions available, see mfun.

Author(s)

Timothy P. Bilton

See Also

BC, FS, IC, mfun

Examples

## Simulate some sequencing data
set.seed(6745)
config <- list(replicate(2,sample(c(1,2,4), size=30, replace=TRUE), simplify=FALSE))
F1data <- simFS(0.01, config=config, meanDepth=10, nInd=50)
## Compute 2-point recombination fractions
F1data$rf_2pt()
## create paternal and maternal linkage groups
F1data$createLG()
## Add BI SNPs
F1data$addBIsnps()
## order Markers
F1data$orderLG(ndim=5)
## Compute Map
F1data$computeMap()

## Produce linkage maps
F1data$plotLM()

tpbilton/GUSMap documentation built on Feb. 22, 2025, 12:27 p.m.