getReadthrough {BioTIP} | R Documentation

## Overlapping Coding Regions

### Description

The `getReadthrough`() function is used to find long transcripts that cover more than two coding regions for gene regions of interst.

### Usage

    getReadthrough(gr, cod_gr)

### Arguments

`gr` | A GRanges object that shows the start and end loci on genome.
`cod_gr` | A GRanges object contaning coding regions.

### Details

For details of findOverlaps, type.partialOverlap, type.50Overlap type.toPlot, queryhits, readthrough and subjecthits see, GenomicRanges https://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html, IRanges https://www.bioconductor.org/packages/release/bioc/html/IRanges.html, and BiocManager http://bioconductor.org/install/index.html.

### Value

A GRanges object that returns overlapping regions of the classified transcript biotypes.

### Note

Replace the path_file when loading data locally to the data directory.

### Author(s)

Zhezhen Wang and Biniam Feleke

### Source

Reference GRCh37 genome https://www.gencodegenes.org/human/release_25lift37.html. For details on gtf format visit ensemble https://useast.ensembl.org/info/website/upload/gff.html.

### References

Wang, Z. Z., J. M. Cunningham and X. H. Yang (2018).'CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs.' Bioinformatics34(17): 664-670'

### Examples

    #First Load datasets and libraries
    library(GenomicRanges)
    data("gencode")
    data("ILEF")
    data("cod")

    # Assigning datasets a GRanges object
    gencode_gr = GRanges(gencode)
    ILEF_gr = GRanges(ILEF)
    cod_gr = GRanges(cod)

    getReadthrough(ILEF_gr,  cod_gr)

    ## Not run: getReadthrough(cod_gr)

[Package BioTIP version 1.1.1 Index]