BgeeDB (version 1.0.2)

makeTable: Formats results of the enrichment test on anatomical structures.

Description

This function loads the results from the topGO test and creates an output table with organ names, fold enrichment and FDR. Data are sorted by p-value and only terms below the specified FDR cutoff are included.

Usage

makeTable(topAnatData, topAnatObject, results, cutoff = 1)

Arguments

topAnatData

A list produced by the function loadTopAnatData().

topAnatObject

An object produced by the function topAnat().

results

A result object, produced by the runtest() function of topGO.

cutoff

An FDR cutoff between 0 and 1. Only terms with FDR lower than this cutoff are included. Default is 1, meaning that all terms are included.

Value

A data frame with significantly enriched anatomical structures, sorted by p-value.

Examples

{
 ## Launch topGO test on data loaded from Bgee
  myTopAnatData <- loadTopAnatData(species = "10090", datatype = "rna_seq")
  geneList <- as.factor(c(rep(0, times=90), rep(1, times=10)))
  names(geneList) <- c("ENSMUSG00000064370", "ENSMUSG00000064368", "ENSMUSG00000064367",
                    "ENSMUSG00000064363", "ENSMUSG00000065947", "ENSMUSG00000064360",
                    "ENSMUSG00000064358", "ENSMUSG00000064357", "ENSMUSG00000064356",
                    "ENSMUSG00000064354", "ENSMUSG00000064351", "ENSMUSG00000064345",
                    "ENSMUSG00000064341", "ENSMUSG00000029757", "ENSMUSG00000079941",
                    "ENSMUSG00000053367", "ENSMUSG00000016626", "ENSMUSG00000037816",
                    "ENSMUSG00000036781", "ENSMUSG00000022519", "ENSMUSG00000079606",
                    "ENSMUSG00000068966", "ENSMUSG00000038608", "ENSMUSG00000047473",
                    "ENSMUSG00000038542", "ENSMUSG00000025386", "ENSMUSG00000028145",
                    "ENSMUSG00000024816", "ENSMUSG00000020978", "ENSMUSG00000055373",
                    "ENSMUSG00000038155", "ENSMUSG00000046408", "ENSMUSG00000030032",
                    "ENSMUSG00000042249", "ENSMUSG00000071909", "ENSMUSG00000039670",
                    "ENSMUSG00000032501", "ENSMUSG00000054252", "ENSMUSG00000068071",
                    "ENSMUSG00000067578", "ENSMUSG00000074892", "ENSMUSG00000027905",
                    "ENSMUSG00000058216", "ENSMUSG00000078754", "ENSMUSG00000062101",
                    "ENSMUSG00000043633", "ENSMUSG00000071350", "ENSMUSG00000021639",
                    "ENSMUSG00000059113", "ENSMUSG00000049115", "ENSMUSG00000053310",
                    "ENSMUSG00000043832", "ENSMUSG00000063767", "ENSMUSG00000026775",
                    "ENSMUSG00000038537", "ENSMUSG00000078716", "ENSMUSG00000096820",
                    "ENSMUSG00000075089", "ENSMUSG00000049971", "ENSMUSG00000014303",
                    "ENSMUSG00000056054", "ENSMUSG00000033082", "ENSMUSG00000020801",
                   "ENSMUSG00000030590", "ENSMUSG00000026188", "ENSMUSG00000014301",
                    "ENSMUSG00000073491", "ENSMUSG00000014529", "ENSMUSG00000036960",
                    "ENSMUSG00000058748", "ENSMUSG00000047388", "ENSMUSG00000002204",
                    "ENSMUSG00000034285", "ENSMUSG00000109129", "ENSMUSG00000035275",
                    "ENSMUSG00000051184", "ENSMUSG00000034424", "ENSMUSG00000041828",
                    "ENSMUSG00000029416", "ENSMUSG00000030468", "ENSMUSG00000029911",
                    "ENSMUSG00000055633", "ENSMUSG00000027495", "ENSMUSG00000029624",
                    "ENSMUSG00000045518", "ENSMUSG00000074259", "ENSMUSG00000035228",
                    "ENSMUSG00000038533", "ENSMUSG00000030401", "ENSMUSG00000014602",
                    "ENSMUSG00000041827", "ENSMUSG00000042345", "ENSMUSG00000028530",
                    "ENSMUSG00000038722", "ENSMUSG00000075088", "ENSMUSG00000039629",
                    "ENSMUSG00000067567", "ENSMUSG00000057594", "ENSMUSG00000005907",
                   "ENSMUSG00000027496")
  myTopAnatObject <- topAnat(myTopAnatData, geneList)
  resFis <- runTest(myTopAnatObject, algorithm = 'elim', statistic = 'fisher')
 ## Format results
  tableOver <- makeTable(myTopAnatData, myTopAnatObject, resFis, 0.1)
}