cash-plotChr: BC, FS and IC method: Heatmap of 2-point rf and LOD estimates...

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

BC, FS and IC method: Heatmap of 2-point rf and LOD estimates from chromosome order

Description

Method for plotting 2-point recombination fraction and LOD score estimates when the SNPs are ordered according to the genomic assembly.

Usage

BCobj$plotChr(parent = "maternal", mat="rf", filename=NULL, chrS=2, lmai=2)
FSobj$plotChr(parent = "maternal", mat="rf", filename=NULL, chrS=2, lmai=2)
ICobj$plotChr(mat="rf", filename=NULL, chrS=2, lmai=2)

Arguments

parent	Character value specifying whether the SNPs segreagting in the maternal parent should be plotted ("maternal"), or whether the SNPs segreagting in the paternal parent should be plotted ("paternal"), or whether all the SNPs should be plotted ("both").
mat	Character value for the matrix to be plotted. "rf" plots the matrix of 2-point recombination fractions while "LOD" plots the matrix of 2-point LOD scores.
filename	Character value giving the name of the file to save the plot to. If NULL, the plot is displayed in the graphics window and not saved to a file.
chrS	Numeric value. Controls the size of the chromosome names on the left side of the plot.
lmai	Numeric value. Controls the amount of white space for the chromosome names on the left side of the plot.

Details

This function plots the heatmap of the matrix of 2-point recombination fraction estimates (or 2-point LOD scores) as computed from the $rf_2pt function when the SNPs are ordered according to the genomic assembly (as given in the VCF file).

Author(s)

Timothy P. Bilton

See Also

BC, FS, IC

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=5, nInd=50) 
## Compute 2-point recombination fractions
F1data$rf_2pt()

## Plot the heatmap
F1data$plotChr()

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