compareAnnot {PloGO2} | R Documentation

## Function to compare annotation percentages

### Description

Compare annotation percentages by means of Fisher's exact test. A reference must be selected, and that name must be amongst the annotation result list names.

### Usage

    compareAnnot(res.list, referenceName, removeZeros = FALSE, correction = TRUE)

### Arguments

`res.list` | List returned by the processAnnotation function
`referenceName` | Name of the condition to compare with
`removeZeros` | Remove the categories with no annotation in them from the result
`correction` | TRUE or FALSE: apply the BH fdr correction to the p-values in each column

### Value

A matrix of p-values or NA. A comparison is made for each sample other than the reference with the reference, and each GO annotation category. The result is not recorded if the annotation numbers were small for that category (<5). This is strictly not needed for Fisher's exact test (though was needed for the chi-square approximation used initially).

### Author(s)

D.Pascovici

### See Also

See Also `processAnnotation`

### Examples

    ## Not run:
    # get list of ID's
    GOIDlist <- GOTermList("BP", 2)

    # find existing files
    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)

    # compare with Control
    compareAnnot(res.list, "Control")

    compareAnnot(res.list, "Control", correction=FALSE)

    ## End(Not run)

[Package PloGO2 version 1.4.0 Index]