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GO term enrichment using goseq

get_enriched_go.Rd

A wrapper function around goseq to perform GO term enrichment analysis. See the goseq documentation for details. pwf can be made using nullp.

Over/underrepresented p-values are automatically adjusted using method = "BH". If gene2cat is not provided then this function will default to using the Homo sapiens genome hg19 and will expect Ensembl gene IDs to have been used to construct the pwf input.

Usage

get_enriched_go(
  pwf,
  gene2cat = NULL,
  ...,
  shorten_term = TRUE,
  shorten_lims = c(1L, 30L),
  filter_no_DE = TRUE
)

Arguments

pwf

data.frame with 3 columns (DEgenes = logical, bias.data = numeric/integer, pwf = numeric) and row names (usually UniProt accessions, Ensembl gene IDs or similar). Typically constructed using nullp.

gene2cat

data.frame with 2 columns containing the mapping between genes (usually UniProt accessions, Ensembl gene IDs or similar) and GO terms. Alternatively, a named list where the names are genes and each entry is a character vector of GO terms.

...

Other arguments to be passed to goseq.

shorten_term

logical. Should an extra column with a substring of the output GO terms be added to the output data.frame? Default is TRUE.

shorten_lims

integer vector of length 2. The start and stop coordinates of the substring.

filter_no_DE

logical. Should terms without any features in the foreground be removed?

Value

Returns a data.frame of over/underrepresented GO terms.