writeAnnotation: Function to print GO/pathway annotation to files

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

Description

Prints available GO or pathway annotation and abundance (if existing) in a long format or an adjacency matrix type format.

Usage

writeAnnotation(res.list, datafile = NULL, datafile.ignore.cols = 1, format = c("list","matrix"),outFolder=tempdir())

Arguments

res.list	The result of processAnnotation
datafile	A CSV file with additional experimental information, if any
datafile.ignore.cols	The number of columns to ignore in the data file
format	Either "matrix" or "list".
outFolder	The output files folder

Details

The GO/pathway information and abundance will be printed to files. If the format is "list", then the files will be text files, and each category will be printed in turn, with all the identifiers and data underneath. If the format is "matrix", then the data will be printed in matrix format, identifiers (rows) by GO categories (columns), with the abundance data appended.

Value

The path of the annotation folder.

Author(s)

D. Pascovici

See Also

processAnnotation

Examples

# choose two simple GO categories
termList <- c("response to stimulus", "transport", "signaling")
GOIDmap <- getGoID(termList)
GOIDlist <- names(GOIDmap)


dir <- system.file("files", package="PloGO2")
file.names <- paste(dir,c("00100.txt", "01111.txt", "10000.txt",
			"11111.txt","Control.txt"), sep="/")

# summarize annotation
res.list <- processAnnotation(file.names, GOIDlist)

# write to "matrix" or alternatively "list" format
writeAnnotation(res.list, format="matrix")

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