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Simon-Coetzee / motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
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Analysis Error Using chek2 Example Data #27

Open DarioS opened 4 years ago

DarioS commented 4 years ago

I am using the example data contained in the package. It fails.

> test <- motifbreakR(snps.indel, hocomoco)
Error in strsplit(as.character(c(snp.sequence.alt.indel, snp.sequence.alt.snv)),  : 
  object 'snp.sequence.alt.indel' not found
In addition: Warning message:
In prepareVariants(fsnplist = snpList, genome.bsgenome = genome.bsgenome,  :
  Indels are included in variant input set, but legacy scoring was enabled.
Legacy scoring is not availble with indels and they will be dropped from analysis

?motifbreakR doesn't contain any useful information about different settings necessary for indels. The Usage section contains legacy.score = TRUE but the Arguments section is missing an entry for legacy.score. All user-modifiable function parameters should be documented in the Arguments section of an R Documentation file. I changed legacy.score to FALSE and another error happened.

> test <- motifbreakR(snps.indel, hocomoco, legacy.score = FALSE)
Error in .local(x, ...) : cluster already started

I think this software needs some thought put into basic tests so it doesn't produce a different error every time you try to use it.

dennishazelett commented 4 years ago

Hi the second error is not caused by motifbreakR