read.annot.file: Function to read an annotation file.
In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description Usage Arguments Details Value Author(s) Examples

Accepts GO id's separated by space or semicolon

1	read.annot.file(fname, format = c("compact","long"))

`fname`	The file name containing GO annotation
`format`	Either `"compact"` or `"long"`; see details

The format is "compact" by default, meaning a text file containing ID's in the first column, and GO 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 tabs, containing an identifier, followed by a GO id, followed optionally by other columns which are ignored. The GO id's will first be aggregated for each identifier. GO files in long format can be obtained using for instance biomart, or GoRetriever.

A data frame with two columns, ID's and GO separated by spaces

T. Keighley, D.Pascovici

# use one of the stored files
dir <- system.file("files", package="PloGO2")
fname <- paste(dir,"00100.txt", sep="/")

# Example with GoRetriever download
longFormat <- paste(dir,"goRetOutput.txt", sep="/")
read.annot.file(fname)
read.annot.file(longFormat, format="long")

# Example with biomart download
biomartDownload <- paste(dir,"mart_export.txt", sep="/")
read.annot.file(biomartDownload, format="long")