readExternalRuns: Read runs from external files

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

Description

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

Usage

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)

Value

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)

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