how do we call 2018 jaspar database? thanks!

[ghost]

[caleblareau]

Here's my attempt at modifying this script from @AliciaSchep -- https://github.com/GreenleafLab/chromVAR/blob/master/R/motifs.R

getJasparMotifs2018 <- function(species = "Homo sapiens", 
                              collection = "CORE", ...) {
  opts <- list()
  opts["species"] <- species
  opts["collection"] <- collection
  opts <- c(opts, list(...))
  out <- TFBSTools::getMatrixSet(JASPAR2018::JASPAR2018, opts)
  if (!isTRUE(all.equal(TFBSTools::name(out), names(out)))) 
    names(out) <- paste(names(out), TFBSTools::name(out), sep = "_")
  return(out)
}
motifs <- getJasparMotifs2018()

@rong923 would you mind trying this function and letting us know if it works?

[Renfang2019]

Thank you. I am on this step as well. Here is the traceback. Any suggestions? 10. value[3L] 9. tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8. tryCatchList(expr, classes, parentenv, handlers) 7. tryCatch(loadNamespace(name), error = function(e) stop(e)) 6. getNamespace(ns) 5. asNamespace(ns) 4. getExportedValue(pkg, name) 3. JASPAR2018::JASPAR2018 2. TFBSTools::getMatrixSet(JASPAR2018::JASPAR2018, opts) 1. getJasparMotifs2018()

[Renfang2019]

Thank you. It worked for the getJasparMotifs2018. Not I got the error,can you please help? motif_ix <- matchMotifs(motifs, counts_filtered,

•                     genome = BSgenome.Mmusculus.UCSC.mm10)
  

dev <- computeDeviations(object = counts_filtered, annotations = motif_ix) Error in nrow(counts_mat) == nrow(background_peaks) : length(bias) == length(fragments_per_peak) is not TRUE