plot_InbreedingChr: Plot Froh-based inbreeding coefficients by group

In detectRUNS: Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

Description

The function plots the distribution of inbreeding/consanguinity coefficients per chromosome and/or group. Three types of plots can be produces: barplots, boxplots, violin plots. With style="All" all three plots are produced.

Usage

plot_InbreedingChr(runs, mapFile, groupSplit = TRUE,
  style = c("ChrBarPlot", "ChrBoxPlot", "FrohBoxPlot", "All"),
  outputName = NULL, plotTitle = NULL, savePlots = FALSE)

Arguments

runs	R object (dataframe) with results on detected runs
mapFile	Plink map file (for SNP position)
groupSplit	plots split by group (defaults to TRUE)
style	type of plot: ChrBarPlot, ChrBoxPlot, FrohBoxPlot, All (all plots)
outputName	title prefix (the base name of graph, if savePlots is TRUE)
plotTitle	title in plot (default NULL)
savePlots	should plots be saved out to files or plotted in the graphical terminal (default)?

Value

plots of the distribution of inbreeding by chromosome and group

Examples

# getting map and ped paths
genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")

# calculating runs of Homozygosity
## Not run: 
# skipping runs calculation
runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1,  minSNP = 15,
ROHet = FALSE,  maxOppositeGenotype = 1, maxMiss = 1,  minLengthBps = 100000,  minDensity = 1/10000)

## End(Not run)
# loading pre-calculated data
runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
runsDF <- readExternalRuns(inputFile = runsFile, program = 'detectRUNS')

plot_InbreedingChr(runs = runsDF, mapFile = mapFile, style='All')

detectRUNS documentation built on Oct. 30, 2019, 11:41 a.m.