GetMotifLoc: Get loci of motif(s).
In mevers/RNAModR: Functional Analysis of RNA Modifications

Description Usage Arguments Details Value Author(s) Examples

Get loci of motif(s) from transcriptome. See 'Details'.

1 2	GetMotifLoc(motif = NULL, refGenome = "hg38", id = NULL, maxMM = 0, showPb = TRUE)

`motif`	A `character` vector; specifies the query sequences that will be matched against the reference transcriptome.
`refGenome`	A character string; specifies the reference genome version; default is `"hg38"`.
`id`	A character string; specifies an identifier for `motif`; default is `NULL`
`maxMM`	An integer scalar; specifies the maximum number of mismatches that are allowed during the motif matching; default is 0.
`showPb`	A logical scalar; if `TRUE` show a progress bar; default is `TRUE`.

Based on a set of query sequences motif, extract the loci of matching sequences within different regions of a reference transcriptome refGenome. The function returns a txLoc object including transcriptomic and genomic loci of the query motif(s). The maximum number of mismatches allowed in the motif search can be adjusted through maxMM. Note that the motif search may take a few minutes, depending on the number of motif(s), hardware, and size of the transcriptome.

A txLoc object.

Maurits Evers, maurits.evers@anu.edu.au

## Not run: 
PAS <- GetMotifLoc(id = "PAS")
PAS <- FilterTxLoc(PAS, c("3'UTR", "CDS", "5'UTR"))
PlotSpatialDistribution(PAS, absolute = FALSE)

## End(Not run)