getReadthrough: Overlapping Coding Regions

In xyang2uchicago/NPS: BioTIP: An R package for characterization of Biological Tipping-Point

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)

xyang2uchicago/NPS documentation built on Dec. 27, 2024, 12:19 p.m.