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hansenlab / minfi

Devel repository for minfi
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gaphunter errors for input class matrix #214

Open BenjaminPlanterose opened 4 years ago

BenjaminPlanterose commented 4 years ago

To whom it may concern,

I have been testing the minfi::gaphunter function and I seem to get errors when I input data from class matrix. I don't get such errors when I input data from class (Genomic)RatioSet or (Genomic)MethylSet. Please see below:

i = 1; set.seed(i); x = rbeta(5, 1, 1); set.seed(i+1); y = rbeta(5, 1, 1); X = rbind(x,y)
gaphunter(X, threshold=0.3, keepOutliers=TRUE) 
# No error

i = 2; set.seed(i); x = rbeta(5, 1, 1); set.seed(i+1); y = rbeta(5, 1, 1); X = rbind(x,y)
gaphunter(X, threshold=0.3, keepOutliers=TRUE)
# Error in apply(diffs, 1, function(x) which(x > threshold)) : dim(X) must have a positive length

i = 3; set.seed(i); x = rbeta(5, 1, 1); set.seed(i+1); y = rbeta(5, 1, 1); X = rbind(x,y)
gaphunter(X, threshold=0.3, keepOutliers=TRUE)
# Error in max(groupanno) : invalid 'type' (list) of argument

# R version 3.6.3 (2020-02-29)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 18.04.4 LTS
# minfi_1.32.0

Please let me know if you need any further information. Cheers, Ben.