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

In BgeeDB/BgeeDB_R: Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

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, ordering = 7)

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.
ordering	A numeric indicating which column should be used to sort the data frame. If the column number is preceded by a \"-\" sign, results are displayed in decreasing ordering. Default is "7", returning data frame sorted by p-values in increasing order.

Value

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

Author(s)

Julien Roux

Examples

{
bgee <- Bgee$new(species="Bos_taurus", dataType="rna_seq")
myTopAnatData <- loadTopAnatData(bgee, stage="UBERON:0000092")
geneList <- as.factor(c(rep(0, times=85), rep(1, times=15)))
names(geneList) <- c("ENSBTAG00000000011","ENSBTAG00000000014","ENSBTAG00000000016",
                     "ENSBTAG00000000026","ENSBTAG00000000039","ENSBTAG00000000040",
                     "ENSBTAG00000000042","ENSBTAG00000000050","ENSBTAG00000000056",
                     "ENSBTAG00000000064","ENSBTAG00000000067","ENSBTAG00000000071",
                     "ENSBTAG00000000072","ENSBTAG00000000080","ENSBTAG00000000081",
                     "ENSBTAG00000000084","ENSBTAG00000000091","ENSBTAG00000000099",
                     "ENSBTAG00000000111","ENSBTAG00000000123","ENSBTAG00000000132",
                     "ENSBTAG00000000153","ENSBTAG00000000162","ENSBTAG00000000163",
                     "ENSBTAG00000000169","ENSBTAG00000000179","ENSBTAG00000000197",
                     "ENSBTAG00000000199","ENSBTAG00000000202","ENSBTAG00000000203",
                     "ENSBTAG00000000204","ENSBTAG00000000213","ENSBTAG00000000215",
                     "ENSBTAG00000000223","ENSBTAG00000000224","ENSBTAG00000000225",
                     "ENSBTAG00000000236","ENSBTAG00000000250","ENSBTAG00000000251",
                     "ENSBTAG00000000252","ENSBTAG00000000253","ENSBTAG00000000261",
                     "ENSBTAG00000000274","ENSBTAG00000000277","ENSBTAG00000000279",
                     "ENSBTAG00000000285","ENSBTAG00000000286","ENSBTAG00000000287",
                     "ENSBTAG00000000289","ENSBTAG00000000297","ENSBTAG00000000305",
                     "ENSBTAG00000000312","ENSBTAG00000000328","ENSBTAG00000000335",
                     "ENSBTAG00000000341","ENSBTAG00000000343","ENSBTAG00000000354",
                     "ENSBTAG00000000355","ENSBTAG00000000356","ENSBTAG00000000365",
                     "ENSBTAG00000000372","ENSBTAG00000000379","ENSBTAG00000000380",
                     "ENSBTAG00000000382","ENSBTAG00000000396","ENSBTAG00000000404",
                     "ENSBTAG00000000405","ENSBTAG00000000406","ENSBTAG00000000411",
                     "ENSBTAG00000000425","ENSBTAG00000000434","ENSBTAG00000000435",
                     "ENSBTAG00000000438","ENSBTAG00000000448","ENSBTAG00000000451",
                     "ENSBTAG00000000454","ENSBTAG00000000456","ENSBTAG00000000457",
                     "ENSBTAG00000000459","ENSBTAG00000000462","ENSBTAG00000000469",
                     "ENSBTAG00000000470","ENSBTAG00000000484","ENSBTAG00000000497",
                     "ENSBTAG00000000501","ENSBTAG00000009707","ENSBTAG00000026266",
                     "ENSBTAG00000021992","ENSBTAG00000005353","ENSBTAG00000005333",
                     "ENSBTAG00000006424","ENSBTAG00000026972","ENSBTAG00000010799",
                     "ENSBTAG00000010799","ENSBTAG00000014614","ENSBTAG00000014614",
                     "ENSBTAG00000045757","ENSBTAG00000046332","ENSBTAG00000046332",
                     "ENSBTAG00000008394")
myTopAnatObject <-  topAnat(myTopAnatData, geneList)
resFis <- runTest(myTopAnatObject, algorithm = 'elim', statistic = 'fisher')
## Format results
tableOver <- makeTable(myTopAnatData, myTopAnatObject, resFis, 0.1)
}

BgeeDB/BgeeDB_R documentation built on Aug. 16, 2024, 9:42 p.m.