detectRUNS R package error

Question

[Roisin Marie]

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
)

Answer 1

[Miika]

I am pretty sure it means you have genotype similar to "A -", which can be illegal. It is an error if "-" (or similar) means missing data, but not if it is a scored deletion.