pathwayEnrichment: Pathway enrichment testing.

In nlhuong/TimeSeriesExperiment: Analysis for short time-series data

Description

This is a wrapper around goana function from limma package for testing over-representation of gene ontology (GO) terms or KEGG pathways in sets of genes.

Usage

pathwayEnrichment(
  object,
  features,
  species,
  feature_column = "feature",
  universe = NULL,
  clustered = TRUE,
  kegg = FALSE,
  ontology = c("BP", "CC", "MF"),
  fltr_DE = 0.1,
  fltr_N = 500,
  fltr_P.DE = 0.05,
  ...
)

Arguments

object	A TimeSeriesExperiment object.
features	A vector of ENTREZID for enrichment testing.
species	A character string specifying the species. See goana for details.
feature_column	the feature column in 'feature.data' slot holding ENTREZIDs, by deafult the 'feature' column.
universe	A vector of genes in the universe. By default all the genes in the 'raw.data' slot.
clustered	Whether features should be grouped based on cluster assignment (stored in [e-mail]$cluster_map) and tested as separate sets.
kegg	Whether KEGG pathways should be used instead of gene ontology (GO)
ontology	character vector of ontologies to be included in output. Elements should be one or more of "BP", "CC" or "MF".
fltr_DE	A scalar fraction of the number of genes in tested set to use as a threshold for filtering genes based on "DE" column (the number of genes in the DE set). Default is 0.1, i.e. at least 0.1 genes in the set must be present in the pathway.
fltr_N	A number of genes used as a threshold to filter out all pathway terms of size greater than the threshold. Default is 500.
fltr_P.DE	A p-value threshold to filter out terms in the enrichment results. Default is 0.05.
...	other parameters for goana or limma::kegga().

Value

a data.frame or list of data.frames with enrichment results.

Examples

data("endoderm_small")
selected_genes <- c('114299', '2825', '3855', '221400', '7941',
                    '6164', '1292', '6161', '6144', '23521')
enrich_res <- pathwayEnrichment(
  object = endoderm_small, clustered = FALSE,
  features = selected_genes,
  species = "Hs", ontology = "BP", fltr_DE = 0,
  fltr_N = Inf, fltr_P.DE = 0.05)
head(enrich_res)

nlhuong/TimeSeriesExperiment documentation built on Sept. 8, 2021, 12:30 a.m.