plot_SnpsInRuns function

Plot the number of times each SNP falls inside runs

Function to plot the number of times/percentage each SNP is inside a run (population-specific signals) against the SNP positions in the genome. Proportions on the y-axis, bps on the x-axis

plot_SnpsInRuns(runs, genotypeFile, mapFile, savePlots = FALSE,
  separatePlots = FALSE, outputName = NULL)

Arguments

• runs: a data.frame with runs per individual (group, id, chrom, nSNP, start, end, length)
• genotypeFile: genotype (.ped) file path
• mapFile: map file (.map) file path
• savePlots: should plots be saved out in files (default) or plotted in the graphical terminal?
• separatePlots: should plots for each chromosome be saved out to separate files?
• outputName: title prefix (the base name of graph, if savePlots is TRUE)

Returns

plot number of times a SNP is in a run by chromosome and population (pdf files)

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
# skipping runs calculation
## Not run:

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 runs per animal (interactive)
plot_SnpsInRuns(runs = runsDF, genotypeFile = genotypeFile, mapFile = mapFile,
savePlots = FALSE, outputName = "ROHom")