processPathFile: Function to process a single pathway file in wego-like native...

In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description

For each pathway extract all ID's from the file. If abundance data is present extract and merge.

Usage

processPathFile(fname, AnnotIDlist, datafile=NULL, datafile.ignore.cols=1, 
	format=c("compact","long"), aggregateFun="sum")	

Arguments

fname	The pathway file name, in either Wego native format or long format
AnnotIDlist	The list of pathway annotation ID
datafile	The file containing abundance or NULL if none.
datafile.ignore.cols	How many columns in the abundance file to ignore. By default assume the first only, containing identifiers.
format	Either "compact" or "long"; see details
aggregateFun	The aggregation function for abundance data

Details

The format is "compact" by default, meaning a text file containing ID's in the first column, and pathway identifiers in the second, separated by spaces or semicolons. This is the same as the "Wego native format". A "long" format is also accepted, meaning a text file with two or more columns separated by spaces, containing an identifier, followed by a pathway id, followed optionally by other columns which are ignored. The pathway id's will first be aggregated for each identifier.

Value

A list with the following components

counts	A vector of the same length as the list of pathway id's of interest giving the number of ID's in each category
ID.list	The list of ID's for each pathway category
datafile	The abundance datafile provided passed through
abundance	A matrix with as many rows as the pathway list provided, and as many columns as the abundance data file
N	The number of protein (gene etc) identifiers in each file
fname	The filename without the file path

Author(s)

J. Wu

Examples

# use one of the stored files
dir <- system.file("files", package="PloGO2")
fname <- paste(dir,"PWFiles/AllData.txt", sep="/")
datafile <- paste(dir, "Abundance_data.csv", sep="/")
AnnotIDlist <- unique(unlist(sapply(read.delim(fname, stringsAsFactors=FALSE)[,2], function(x) strsplit(x, split=" ")[[1]])))


# or if abundance in present aggregate that by category
processPathFile(fname, AnnotIDlist, datafile=datafile)

PloGO2 documentation built on Nov. 8, 2020, 5:40 p.m.