compareAnnot: Function to compare annotation percentages
In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description Usage Arguments Value Author(s) See Also Examples

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.

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

`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

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).

D.Pascovici

See Also processAnnotation

## 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)