readExternalRuns function

Read runs from external files

Function to read in, from external files, the output of software for ROH:

1. detectRUNS: output saved out to a file (e.g. write.table)
2. Plink: output from the --homozyg option (.hom files)
3. BCFtools: output from the roh option

readExternalRuns(inputFile = NULL, program = c("plink", "BCFtools",
  "detectRUNS"))

Arguments

• inputFile: name of (path to) external file
• program: source program that produced the ROH file (one of detectRUNS, Plink, BCFtools)

Returns

dataframe in the correct format to be used with plots and statistics functions from detectRUNS

Examples

# getting map and ped paths
## Not run:

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

# calculating runs of Homozygosity
runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1,  minSNP = 15,
ROHet = FALSE,  maxMissRun = 1, maxMissWindow = 1,  minLengthBps = 100000,  minDensity = 1/10000)

write.table(x= runs,file = 'RunsFileTest.txt', quote=F, row.names = F)
newData=readRunsFromFile(runsFile = 'RunsFileTest.txt', program = 'detectRUNS')
## End(Not run)