This function forms genesets basing on the differential expression result, and calls gene ontology (GO) analysis method provided by gprofiler2.
runGOEnrich(
result,
group = NULL,
useBg = TRUE,
orderBy = NULL,
logFCThresh = 1,
padjThresh = 0.05,
splitReg = FALSE,
...
)
A list object where each element is a result list for a group. Each result list contains two elements:
data.frame of main GO analysis result.
Meta information for the query.
See gprofiler2::gost()
. for detailed explanation.
Data frame of unfiltered output from runMarkerDEG
or runPairwiseDEG
.
Selection of one group available from result$group
.
Default NULL
uses all groups involved in DE result
table.
Logical, whether to set all genes involved in DE analysis
(before threshold filtering) as a domain background of GO analysis. Default
TRUE
. Otherwise use all annotated genes from gprofiler2 database.
Name of DE statistics metric to order the gene list for each
group. Choose from "logFC"
, "pval"
or "padj"
to enable
ranked mode. Default NULL
to use two-list mode.
The absolute valued log2FC threshold above which the
genes will be used. Default 1
.
The adjusted p-value threshold less than which the genes
will be used. Default 0.05
.
Whether to have queries of both up-regulated and
down-regulated genes for each group. Default FALSE
only queries
up-regulated genes and should be preferred when result
comes from
marker detection test. When result
comes from group-to-group DE test,
it is recommended to set splitReg = TRUE
.
Additional arguments passed to gprofiler2::gost()
. Useful
ones are:
organism
The organism to be used for the analysis. "hsapiens" for human, "mmusculus" for mouse.
evcodes
Whether to include overlapping genes for each term.
Default FALSE
.
significant
Whether to filter out non-significant terms.
Default TRUE
.
Arguments query
, custom_bg
, domain_scope
, and
ordered_query
are pre-specified by this wrapper function.
GO term enrichment test often goes with two modes: two-list mode and ranked mode.
Two-list mode comes with a query gene set and a background gene set.
A query gene set contains the filtered DEGs in this analysis. A background
can be all the genes involved in the DEG test (default, useBg = TRUE
),
or use all annotated genes in the gprofiler2 database (useBg = FALSE
).
Ranked mode comes with only one query gene set, which is sorted. It should
contain the whole domain background genes while significant genes are
supposed to come first. Set orderBy
to one of the DE statistics metric
to enable this mode. useBg
will be ignored in this mode.
Kolberg, L. et al, 2020 and Raudvere, U. et al, 2019
# \donttest{
if (requireNamespace("gprofiler2", quietly = TRUE)) {
go <- runGOEnrich(deg.pw)
}
# }
Run the code above in your browser using DataLab