Data Import Issue detectRUNS R

Question

[Whirlingdaf]

I am running into an issue when importing data with detectRUNS in R.

The following commands to import PLINK files have not been successful, and result in blank data frames.

genotypeFilePath <- system.file("extdata", "genome.ped",package="detectRUNS")
mapFilePath <- system.file("extdata", "genome.map", package="detectRUNS")

head(genotypeFilePath)
[1] ""

The PLINK data are correctly formatted.

OR

I also attempted to import ROH data from bcftools, with the same result.

savedRunFile <- system.file("extdata", "ROH", package="detectRUNS")
runs <- readExternalRuns(inputFile = savedRunFile, program = "BCFtools")
head(runs)

The bcftools output seems to be correct as well:

# RG    [2]Sample       [3]Chromosome   [4]Start        [5]End  [6]Length (bp)  [7]Number of markers    [8]Quality (average fwd-bwd phred score)
# ST    [2]Sample       [3]Chromosome   [4]Position     [5]State (0:HW, 1:AZ)   [6]Quality (fwd-bwd phred score) 
ST      C_101 chr1    2527    1       3.0 
ST      C_101 chr1    2537    1       37.5

However I still end up with no data successfully imported

head(readExternalRuns) 
[1] ""

Any insight would be greatly appreciated. Thank you!

[bk11]

Where are your genome.ped/map files located? You need to provide path to your map and genotype types files like this-

genotypeFilePath <- "/pathToYourGenotype/genome.ped"
mapFilePath <- "/pathToYourGenotype/genome.map"

[Whirlingdaf]

Thanks, they are actually within the working directory. But I also added the full path just in case, with the same result...

Answer 1

[bk11]

You providing just path to your .ped and .map files and reading them. Therefore head(genotypeFilePath) will show you nothing.

[Whirlingdaf]

Ah, I see! I was confused as I was following the workflow suggested in the vignette. Thank you.

[Ram]

I've moved bk11's comment to an answer. Please accept it to mark the post as solved.