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.
get_enriched_go(
pwf,
gene2cat = NULL,
...,
shorten_term = TRUE,
shorten_lims = c(1L, 30L)
)
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
.
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
.
logical
. Should an extra column with a substring of
the output GO terms be added to the output data.frame? Default is TRUE
.
integer vector
of length 2. The start and stop
coordinates of the substring.
Returns a data.frame
of over/underrepresented GO terms.