bpTrack: Visualization: generating tracks for 'igvR' (per bp)

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

Visualization: generating tracks for igvR (per bp)

Description

This function outputs a list of GRanges format objects of ribosome P-site footprints per bp. It can be used for igvR visualization.

Usage

bpTrack(data, names.rep = NULL, genes.list)

Arguments

data	Data object from psiteMapping function or wrapper function RiboDiPA.
names.rep	Customized names of the replicates. Default value uses the column names of data$counts.
genes.list	A list of genes for visualization. Default value uses all genes listed in data$coverage

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 GRanges format objects. Each element is a GRanges object of the P-site footprint tracks of selected genes.

Examples

data(data.psite)
names.rep <- c("mutant1", "mutant2", "wildtype1", "wildtype2")
tracks.bp <- bpTrack(data = data.psite, names.rep = names.rep, 
    genes.list = c("YDR050C", "YDR062W", "YDR064W"))

# library(igvR)
# igv <- igvR()
# setBrowserWindowTitle(igv, "ribosome footprint track example")
# setGenome(igv, "saccer3")
# for(track.name in names.rep){
#     track.rep <- tracks.bp[[track.name]]
#     track <- GRangesQuantitativeTrack(trackName = paste(track.name, "bp"),
#         track.rep[,1], color = "green")
#     displayTrack(igv, track)
# }

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