Entering edit mode
20 months ago
Roisin Marie
•
0
Hi,
I am using the R package 'detectRUNS', and when I try to run it on my data I get this error:
You are using the method: SLIDING WINDOWS
Analysing Runs of Homozygosity (ROHom)
Window size: 15
Threshold for calling SNP in a Run: 0.05
Error in pedConvertCpp(genotype[7:length(genotype)]) :
Found only one allele missing in a pair
I can't find anything about this error online, is someone able to explain what's going on?
Thanks- I have copied my parameters below:
sample_sliding = slidingRUNS.run(
genotypeFile = "Input/HomMap/sample.ped",
mapFile = "Input/HomMap/sample.map",
windowSize = 15,
threshold = 0.05,
ROHet = FALSE,
maxOppWindow = 1,
maxMissWindow = 1,
maxGap = 10^6,
minLengthBps = 250000,
minDensity = 1/10^3,
maxOppRun = NULL,
maxMissRun = NULL
)