viewKegg: Compare KEGG pathways between two functional annotation...

In sam-bassett/CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

Description

viewKegg uses pathview to compare the gene lists visually by KEGG pathway. You can either supply a pathway id or the function will pick the most differentially enriched pathway between the two inputs. As functional annotation charts don't have differential gene expression information, a boolean scale is used - genes in the pathway are coloured green if from setA, yellow if from both, and red if from setB. We recommend you supply a working directory, as pathview will download an XML and PNG file as well as output an additional PNG of the pathway.

Usage

viewKegg(setA, setB, keggTerm = NULL, species = NULL, workingDir = NULL,
  sortByCount = FALSE, ...)

Arguments

setA	FunctionalAnnotationChart to compare
setB	FunctionalAnnotationChart to compare
keggTerm	If a specific KEGG pathway is of interest, input the name here; otherwise, the most differentially expressed pathway will be used.
species	The program can usually figure out the species from the KEGG terms, but if it can't, supply the species ID here. From pathview vignette, run 'data(bods); bods' to find species codes.
workingDir	The directory to output into. Recommended, since pathview will put a few different files there each time.
sortByCount	Set TRUE if you want the function to automatically choose the pathway with the most number of genes
...	Arguments to be passed to pathview

Value

Output from pathview: a list of 2, plot.data.gene and plot.data.cpd

Examples

## Not run: 
# Since this function requires writing to a directory, it won't be run here
data(funChart1)
data(funChart2)
viewKegg(funChart1, funChart2)

## End(Not run)

sam-bassett/CompGO documentation built on May 29, 2019, 1:01 p.m.