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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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object 'snp.sequence.alt.indel' not found #19

Open yfu1116 opened 4 years ago

yfu1116 commented 4 years ago

Hi,

I took motifbreakR 2.0.0 to perform the analysis of indel, while I got an error here:

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

The code I used:

snps.indel.vcf <- system.file("extdata", "chek2.vcf.gz", package = "motifbreakR")
snps.indel <- variants.from.file(file = snps.indel.vcf, 
                                 search.genome = BSgenome.Hsapiens.UCSC.hg19, 
                                 format = "vcf")

results <- motifbreakR(snps.indel[1:5], filterp = TRUE,
                       pwmList = hocomoco,
                       threshold = 1e-4,
                       method = "ic",
                       bkg = c(A=0.25, C=0.25, G=0.25, T=0.25),
                       BPPARAM = BiocParallel::bpparam())

I guess there should be an option to get 'snp.sequence.alt.indel', but I didn't see it in the vignette.