detectMotifs: Detect over-represented motifs
In mengchen18/PTMotif: Detect PTM motifs

Description Usage Arguments Details Value Author(s)

Detect over-represented motifs

detectMotifs(fg.seqs, bg.seqs, fg.genes = NULL, bg.genes = NULL,
  method = c("cvp", "all")[1], min.seqs = 5, max.pvalue = 1e-06,
  max.gw.pvalue = NULL, center = "STY", ncores = 1, verbose = TRUE,
  annotate = FALSE)

`fg.seqs`	a character vector of foreground sequences
`bg.seqs`	a character vector of background sequences
`fg.genes`	character vector of gene names of foreground sequences, it should have the same length as `fg.seqs`
`bg.genes`	character vector of gene names of background sequences, it should have the same length as `bg.seqs`
`method`	the algorithm used to detect potential motifs, multiple are allowed
`min.seqs`	the minimum frequency of a motif should be considered
`max.pvalue`	the maximum FDR to be reported
`max.gw.pvalue`	the maximum p value of on gene wise to be reported, only useful when both `fg.genes` and `bg.genes` are specified
`center`	the amino acid centered at the sequences, sequences with other center AA would be removed from the list. To disable this function, set `center = NULL`. Only used in `checkSeqs` and `motif_all`.
`ncores`	the number of cores to be used, passed to `mclapply`.
`verbose`	logical, whether print message
`annotate`	whether the discovered motif should be annotated by known motifs