processAnnotation: Function to process a set of annotation files given a list of...
In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description Usage Arguments Details Value Author(s) See Also Examples

For each file in the list extract all identifiers that belong to each GO or pathway category in the list of identifiers. An identifier “belongs” to a GO or pathway category if it is annotated at the category itself or any of its children in the GO graph.

1 2	processAnnotation(file.list, AnnotIDlist, data.file.name = NULL, printFiles = FALSE, format = c("compact","long"), datafile.ignore.cols = 1, aggregateFun="sum")

`file.list`	A list of files
`AnnotIDlist`	A list of GO/pathway identifiers
`data.file.name`	A list containing additional data such as abundance information
`printFiles`	TRUE/FALSE If true an annotation summary file is generated for each input file
`format`	One of “compact” by default or or “long”, the format of the annotation files. See details.
`datafile.ignore.cols`	How many columns in the abundance file to ignore. By default assume the first only, containing identifiers.
`aggregateFun`	Either "sum" or "product"; the aggregation operation for abundance data

The format is for the GO/pathway files is “compact” by default, meaning a text file containing ID's in the first column, and GO/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 GO/pathway id, followed optionally by other columns which are ignored. The GO/pathway id's will first be aggregated for each identifier.

A list of the same length as the list of files submitted. Each list element is the result of processGoFile or processPathFile.

D. Pascovici, J.Wu

processGoFile, processPathFile

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


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

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

# files in long format
longFormat <- file.path(path,  "goRetOutput.txt")
processAnnotation(longFormat, GOIDlist, format = "long")

# For KEGG pathway analysis
fname <- file.path(path,"PWFiles", "red.txt")
datafile <- file.path(path,"Abundance_data.csv")

AnnotIDlist <- c("osa01100","osa01110","osa01230","osa00300","osa00860")
		
res.list <- processAnnotation(fname, AnnotIDlist,  data.file.name = datafile)