motif_finding_notes.txt

This workshop originally used motifRG, however it has been removed from Bioconductor.

The only Bioconductor motif finder now seems to be rGADEM. It seems to have build problems, plus only runs in unstranded mode.

I've decided it's better to emphasize using an external program, from the MEME suite.


This is the old motifRG code:

```{r cache=TRUE, warning=FALSE, message=FALSE}
library(motifRG)


# Generate a background set of sequences by shuffling bases
# - calling sample() on a DNAString shuffles it
background_seqs <- endoapply(initiation_seqs, sample)
# Equivalent to:
# background_seqs <- DNAStringSet( lapply(initiation_seqs, sample) )

names(background_seqs) <- paste0(names(background_seqs), "-shuffled")


results <- findMotifFgBg(
    initiation_seqs, background_seqs, 
    both.strand=FALSE, start.width=4)

summaryMotif(results$motif, results$category)

motifHtmlTable(results)

refined <- refinePWMMotif(results$motifs[[1]]@match$pattern, initiation_seqs)
seqLogo(refined$model$prob)
```