processAnnotation {PloGO2} | R Documentation

## Function to process a set of annotation files given a list of GO/pathway identifiers of interest

### Description

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.

### Usage

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

### Arguments

`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

### Details

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.

### Value

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

### Author(s)

D. Pascovici, J.Wu

### See Also

`processGoFile`, `processPathFile`

### Examples

    # 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)

[Package PloGO2 version 1.6.0 Index]