writeAnnotation {PloGO2} | R Documentation |
Prints available GO or pathway annotation and abundance (if existing) in a long format or an adjacency matrix type format.
writeAnnotation(res.list, datafile = NULL, datafile.ignore.cols = 1, format = c("list","matrix"),outFolder=tempdir())
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 |
outFolder |
The output files folder |
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.
The path of the annotation folder.
D. Pascovici
# 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")