SmartMap: Map genome coordinates to transcript coordinates.
In mevers/RNAModR: Functional Analysis of RNA Modifications

Description Usage Arguments Details Value Author(s) Examples

Map genome coordinates to transcript coordinates.

1 2	SmartMap(gr, id = NULL, refGenome = "hg38", ignore.strand = FALSE, showPb = TRUE)

`gr`	A `GRanges` object; specifies the list of of genomic features to be mapped.
`id`	A `character` string; specifies a name for loci from `gr`; if `NULL` then `id = ""`; default is `NULL`.
`refGenome`	A `character` string; specifies a specific reference genome assembly version based on which the matching transcriptome is loaded; default is `"hg38"`.
`ignore.strand`	A `logical` scalar; if `TRUE` strand information is ignored when mapping genome coordinates to transcript coordinates; default is `FALSE`.
`showPb`	A `logical` scalar; if `TRUE` show a progress bar; default is `TRUE`.

The function maps genomic coordinates from locus to transcript section coordinates. The function automatically loads a reference transcriptome based on refGenome. An error is produced if a reference transcriptome could not be found. This usually means that BuildTx was not yet run successfully. The function returns a txLoc object of mapped positions.

A txLoc object. See 'Details'.

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

## Not run: 
bedFile <- system.file("extdata",
                       "miCLIP_m6A_Linder2015_hg38.bed",
                       package = "RNAModR")
sites <- ReadBED(bedFile)
txSites <- SmartMap(sites, id = "m6A", refGenome = "hg38")

## End(Not run)