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 )