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ge11232002 / TFBSTools

Software Package for Transcription Factor Binding Site (TFBS) Analysis
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getMatrixSet is incompatable with JASPAR2024 #39

Open mossconfuse opened 5 months ago

mossconfuse commented 5 months ago

I tried running 

JASPAR2024 <- JASPAR2024::JASPAR2024()
pfm <- getMatrixSet(
  x = JASPAR2024,
  opts = list(collection = "CORE", tax_group = 'plants', all_versions = FALSE)
)

but got an error:

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘getMatrixSet’ for signature ‘"JASPAR2024"’

My workaround seems to work, but perhaps TFBSTools needs to be updated for JASPAR2024 compatibility?

JASPAR <- JASPAR2020::JASPAR2020
JASPAR@db <- JASPAR2024::JASPAR2024() %>% .@db

pfm <- getMatrixSet(
  x = JASPAR,
  opts = list(collection = "CORE", tax_group = 'plants', all_versions = FALSE)
)
ghost commented 4 months ago

Or alternatively, one can simply do:

jaspar <- JASPAR2024::JASPAR2024()
getMatrixSet(jaspar@db, ...)