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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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No motifbreakR Results for chek2 Analysis #29

Open DarioS opened 4 years ago

DarioS commented 4 years ago

Using the example VCF file provided with the package, I get no results, even if I set threshold to zero which should return lots of false positives.

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(snpList = snps.indel[1:50], threshold = 0, pwmList = hocomoco, legacy = FALSE, BPPARAM = SerialParam())

Warning message:
  No SNP/Motif Interactions reached threshold

It it a bug?

danielcgingerich commented 2 years ago

same issue here