wsnp_Ku_rep_c103074_89904851: Raw genotyping data for marker wsnp_Ku_rep_c103074_89904851

In mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

Raw genotyping data for marker wsnp_Ku_rep_c103074_89904851

Author(s)

Alex Whan, Matthew Morell, Rohan Shah, Colin Cavanagh This dataset contains the raw genotyping data for marker wsnp_Ku_rep_c103074_89904851. This marker is interesting, because it can be mapped to both chromosome 1B (four alleles) and 1D (two alleles).

Examples

data(eightParentSubsetMap)
data(wsnp_Ku_rep_c103074_89904851)
data(callFromMapExampleLocalisationStatistics)
called <- callFromMap(rawData = as.matrix(wsnp_Ku_rep_c103074_89904851), existingImputations = 
    eightParentSubsetMap, useOnlyExtraImputationPoints = TRUE, tDistributionPValue = 0.8, 
    thresholdChromosomes = 80, existingLocalisationStatistics = existingLocalisationStatistics)
library(ggplot2)
library(gridExtra)
plotData <- wsnp_Ku_rep_c103074_89904851
plotData$genotype1B <- factor(called$classificationsPerPosition$Chr1BLoc31$finals)
plotData$imputed1B <- factor(imputationData(eightParentSubsetMap)[, "Chr1BLoc31"])
plotData$genotype1D <- factor(called$classificationsPerPosition$Chr1DLoc16$finals)
plotData$imputed1D <- factor(imputationData(eightParentSubsetMap)[, "Chr1DLoc16"])

plotImputations1B <- ggplot(plotData, mapping = aes(x = theta, y = r, color = imputed1B)) + 
    geom_point() + theme_bw() + ggtitle("Imputed genotype, 1B") + 
    guides(color=guide_legend(title="IBD genotype"))

called1B <- ggplot(plotData, mapping = aes(x = theta, y = r, color = genotype1B)) + 
    geom_point() + theme_bw() + ggtitle("Called genotype, 1B") + 
    guides(color=guide_legend(title="Called cluster")) + scale_color_manual(values = 
    c("black", RColorBrewer::brewer.pal(n = 4, name = "Set1")))

plotImputations1D <- ggplot(plotData, mapping = aes(x = theta, y = r, color = imputed1D)) + 
    geom_point() + theme_bw() + ggtitle("Imputed genotype, 1D") + 
    guides(color=guide_legend(title="IBD genotype"))

called1D <- ggplot(plotData, mapping = aes(x = theta, y = r, color = genotype1D)) + 
    geom_point() + theme_bw() + ggtitle("Called genotype, 1D") + 
    guides(color=guide_legend(title="Called cluster")) + 
    scale_color_manual(values = c("black",RColorBrewer::brewer.pal(n=3,name = "Set1")[1:2]))

grid.arrange(plotImputations1B, plotImputations1D, called1B, called1D)

mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.