exonTrack: Visualization: generating tracks for 'igvR' (per exon)

In jipingw/RiboDiPA: Differential pattern analysis for Ribo-seq data

Visualization: generating tracks for igvR (per exon)

Description

This function outputs a list of GRanges format objects of ribosome P-site footprints per exon, as well as corresponding test results. It can be used for igvR visualization.

Usage

exonTrack(data, gene)

Arguments

data	Data object from diffPatterbTestExon function or wrapper function RiboDiPA.
gene	One gene for visualization at a time, since different genes have different number of transcripts.

Details

R package igvR is not implemented in RiboDiPA. Users need install igvR through Bioconductor or relevant source package. A simple illustration example of how to use it for igvR visualization is given below.

Value

A list of lists. Each element is a list of GRanges objects representing replicates. Each second level list element is P-site footprint count per exon with differential pattern test results in a transcript.

Examples

data(result.exon)
tracks.exon <- exonTrack(data = result.exon, gene = "tY(GUA)D")

# library(igvR)
# igv <- igvR()
# setBrowserWindowTitle(igv, "ribosome footprint per exon example")
# setGenome(igv, "saccer3")

# for(track.name in names(tracks.exon)){
#     track.rep <- tracks.exon[[track.name]]
#     for(tx.name in names(track.rep)){
#         track.tx <- tracks.exon[[track.name]][[tx.name]]
#         track <- GRangesQuantitativeTrack(trackName = 
#             paste(track.name, tx.name), track.tx[,1], color = track.name)
#         displayTrack(igv, track)
#     }
# }

jipingw/RiboDiPA documentation built on Dec. 10, 2024, 8:46 p.m.