plot_manhattanRuns: Plot the proportion of times SNPs are inside runs - MANHATTAN...

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

Description

Function to plot the proportion of times/percentage each SNP in inside a run (population-specific signals) against SNP position in all chromosomes together Proportions on the y-axis, bps on the x-axis for all analysed chromosomes This is similar to the familiar GWAS Manhattan plot

Usage

plot_manhattanRuns(runs, genotypeFile, mapFile, savePlots = FALSE,
  outputName = NULL, plotTitle = 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?
outputName	title prefix (the base name of graph, if savePlots is TRUE)
plotTitle	title in plot (default)

Value

Manhattan plots of proportion of times SNPs are inside runs, per 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
## 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 runs per animal (interactive)
plot_manhattanRuns(runs = runsDF, genotypeFile = genotypeFile, mapFile = mapFile,
savePlots = FALSE, plotTitle = "ROHom")

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