goseqTable: Extract functional terms enriched in the DE genes, based on...

In federicomarini/ideal: Interactive Differential Expression AnaLysis

Extract functional terms enriched in the DE genes, based on goseq

Description

A wrapper for extracting functional GO terms enriched in a list of (DE) genes, based on the algorithm and the implementation in the goseq package

Usage

goseqTable(
  de.genes,
  assayed.genes,
  genome = "hg38",
  id = "ensGene",
  testCats = c("GO:BP", "GO:MF", "GO:CC"),
  FDR_GO_cutoff = 1,
  nTop = 200,
  orgDbPkg = "org.Hs.eg.db",
  addGeneToTerms = TRUE
)

Arguments

de.genes	A vector of (differentially expressed) genes
assayed.genes	A vector of background genes, e.g. all (expressed) genes in the assays
genome	A string identifying the genome that genes refer to, as in the goseq::goseq() function
id	A string identifying the gene identifier used by genes, as in the goseq::goseq() function
testCats	A vector specifying which categories to test for over representation amongst DE genes - can be any combination of "GO:CC", "GO:BP", "GO:MF" & "KEGG"
FDR_GO_cutoff	Numeric value for subsetting the results
nTop	Number of categories to extract, and optionally process for adding genes to the respective terms
orgDbPkg	Character string, named as the org.XX.eg.db package which should be available in Bioconductor
addGeneToTerms	Logical, whether to add a column with all genes annotated to each GO term

Details

Note: the feature length retrieval is based on the goseq::goseq() function, and requires that the corresponding TxDb packages are installed and available

Value

A table containing the computed GO Terms and related enrichment scores

Examples

library("airway")
data("airway", package = "airway")
airway
dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
  colData = colData(airway),
  design = ~ cell + dex
)
dds_airway <- DESeq2::DESeq(dds_airway)
res_airway <- DESeq2::results(dds_airway)

res_subset <- mosdef::deresult_to_df(res_airway)[1:100, ]
myde <- res_subset$id
myassayed <- rownames(res_airway)
## Not run: 
mygo <- goseqTable(myde,
  myassayed,
  testCats = "GO:BP",
  addGeneToTerms = FALSE
)
head(mygo)

## End(Not run)

federicomarini/ideal documentation built on Dec. 21, 2024, 8:46 p.m.