term_enrichment_by_subset: term_enrichment_by_subset

Description Usage Arguments Value Examples

View source: R/lib_enrichment.R

Description

Run enrichment simultaneously across a group of prioritized gene lists. For example, in a time course dataset, one may have a different list of genes that are differentially expressed at each time point. This function facilitates rapid evaluation of term enrichment across time point comparisons. Alternatively, one may have a different list of differentially expressed genes by drug treatment, environmental condition, ect.

Usage

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term_enrichment_by_subset(groups = NA, resources = resources.default,
  q_value_threshold = 0.01, verbose = TRUE, display_type = "q",
  phred = TRUE, ...)

Arguments

groups

A list() of genes for enrichment. Each entry in the list() is an input set of genes. Enrichment is performed for each of these entries.

resources

character vector for which resources to use in enrichment

q_value_threshold

minimum q-value (FDR adjusted p-value) in any group for the term to be included in results

verbose

print additional status updates on what the function is doing

display_type

Flag for which data type will be returned. One of "q" (default) for q-values, "p" for unadjusted p-values, or "n" for the number of genes overlapping the term.

phred

Logical flag (default TRUE) to return the -log10 of p/q values

...

Further arguments are passed on to enrichment_symbols()

Value

Returns a term-by-study matrix of enrichment values (value determined by "display_type")

Examples

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## Create list of gene sets to evaluate.
##   This example is from a vaccine study where we pre-generated differentially expressed genes.
##   This object will be passed to the groups parameter.
require(RITANdata)
vac1.de.genes <- list(vac1.day0vs31.de.genes, vac1.day0vs56.de.genes)
names(vac1.de.genes) <- c("Day0vs31", "Day0vs56")
print(str(vac1.de.genes))

## Not run: 
## Run term_enrichment_by_subset on the two results.
##   This function usually takes a few seconds to a minute to run.
m <- term_enrichment_by_subset(groups = vac1.de.genes, q_value_threshold = .9)
summary(m)
plot( m, label_size_y = 4, show_values = FALSE )

## End(Not run)

MTZimmer/RITAN documentation built on Oct. 11, 2018, 10:17 a.m.