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

Description Usage Arguments Details Value Author(s)

Map genome coordinates to transcript coordinates. See 'Details'. This is a low-level function that is being called from SmartMap. There is no guarantee that this function will get exported in future releases of RNAModR. Use at your own risk.

1 2	SmartMap.ToTx(gr, txBySec, seqBySec, geneXID, ignore.strand = FALSE, showPb = FALSE)

`gr`	A `GRanges` object; specifies the list of genomic features to be mapped.
`txBySec`	A `list` of `GRangesList` objects; specifies the reference transcriptome; the object is usually a result of running `BuildTx`.
`seqBySec`	A `list` of `DNAStringSet` objects; sequences of (some or all) segments from `txBySec`; the object is usually a result of running `BuildTx`.
`geneXID`	A `DataFrame`; specifies different gene IDs; the object is usually a result of running `BuildTx`.
`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 `FALSE`.

The function maps genomic coordinates from gr to transcript region coordinates from txBySec. The function returns a list of DataFrame objects, each with the following columns:

locus_in_txx_region: A GRanges object
locus_in_genome: A GRanges object
score: A numeric vector
id: A character vector
tx_region: A character vector
tx_region_width: An integer vector
tx_region_sequence: A DNAStringSet object
tx_refseq: A character vector
gene_entrez: A character vector
gene_symbol: A character vector
gene_ensembl: A character vector
gene_name: A character vector