cash-plotSyn: BC, FS and IC method: Produce synteny plot

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

BC, FS and IC method: Produce synteny plot

Description

Method for plotting the combined linkage group SNP ordering against the original SNP order from the genomic assembly.

Usage

BCobj$plotSyn()
FSobj$plotSyn()
ICobj$plotSyn()

Details

This function produces a scatter plot of the SNP order as obtained from the linkage analysis against the SNP order given by the genomic assembly.

BC object: The SNP order from the linkage analysis is from the pseudo-testcross linkage groups with BI SNPs constructed from the addBIsnps function and ordered via the $orderLG function.

FS object: The SNP order from the linkage analysis is from the combined linkage groups obtained from the $addBIsnps function and ordered via the $orderLG function.

IC object: The SNP order from the linkage analysis is from the linkage groups computed from the $computeLG function and ordered via the $orderLG function.

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=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)

## Plot synteny plot
F1data$plotSyn()

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