getURL: Highlight the relevant genes for a specific pathway in its...

In sigora: Signature Overrepresentation Analysis

Highlight the relevant genes for a specific pathway in its pathway diagram

Description

This function highlights the genes involved in the present GPS for a pathway of interest in its diagram. Please note that this functionality is only implemented for results of Reactome or KEGG based analyses.

Usage

getURL(yy, i)

Arguments

yy	A sigora analysis result object (created by sigora).
i	The rank position of the pathway of interest in summary_results.

Value

The URL of the pathway diagram, where the relevant genes from your original query list are highlighted.

See Also

sigora

Examples

data('kegH')
set.seed(seed=12345)
a1<-genesFromRandomPathways(kegH,3,50)
## originally selected pathways:\cr
a1[["selectedPathways"]]
## what are the genes
a1[["genes"]]
## sigora's results with this input:\cr
sigoraRes <- sigora(GPSrepo =kegH, queryList = a1[["genes"]],level = 2)
## Diagram for the most significant result, where the genes from our list are highlighted in red:
getURL(sigoraRes,1)

sigora documentation built on March 18, 2022, 8:05 p.m.