plot_PatternRuns: Plot sum of run-lengths (or average run-lengths) against the...

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

Description

Function to plot the sum of run lengths (or the average run length) per individual against the average number of runs per individual. Points can be differentially coloured by group/population. This plot can be useful to identify patterns in the distribution of runs in different groups (e.g. few long runs vs many short runs)

Usage

plot_PatternRuns(runs, mapFile, method = c("sum", "mean"),
  outputName = NULL, savePlots = FALSE, plotTitle = NULL)

Arguments

runs	a data.frame with runs per individual (group, id, chrom, nSNP, start, end, length)
mapFile	map file (.map) file path
method	"sum" or "mean" of run lengths per individual sample
outputName	title prefix (the base name of graph, if savePlots is TRUE)#'
savePlots	should plots be saved out to files or plotted in the graphical terminal (default)?
plotTitle	title in plot (default NULL)

Value

plot of number of runs vs run-length sum/mean per individual sample

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_PatternRuns(runs = runsDF, mapFile = mapFile, method = 'sum')
plot_PatternRuns(runs = runsDF, mapFile = mapFile, method = 'mean')

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