readExternalRuns {detectRUNS} | R Documentation |
Read runs from external files
Description
Function to read in, from external files, the output of software for ROH:
-
detectRUNS
: output saved out to a file (e.g. write.table) -
Plink
: output from the--homozyg
option (.hom
files) -
BCFtools
: output from theroh
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 |
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)
[Package detectRUNS version 0.9.6 Index]