DEVis (version 1.0.1)

enrich_res: Incorporate additional data about differentially expressed genes into a DESeq2 result set.

Description

Given a DESeq result set, as generated with DESeq2::results(), this function adds several additional components to the object. Variables created are numDE, numUp, numDown, allNames, upNames, and downNames, allDE, upDE, downDE, case, control, contrast, and designField. All calculations are performed based on significance thresholds set using the init_cutoffs() function. This function is typically used as a helper function for data aggregation.

Usage

enrich_res(res, lfc_filter = FALSE)

Arguments

res

A DESeq2 result set as generated through DESeq2::results(). Must be a DESeq object of type S4.

lfc_filter

Should the enrichment apply LFC filtering or not. Boolean.

Value

An expanded DESeq result set of type DESeqResMeta containing the following fields: [numDE, numUp, numDown, allNames, upNames, and downNames, allDE, upDE, downDE, case, control, contrast, and designField]

See Also

init_cutoffs

Examples

# NOT RUN {
#Enrich a result set. This will make several new data points available.
res.day1 <- results(dds, contrast=c("Condition_Time", "day1_disease", "day1_control"))
enriched_result <- enrich_res(res.day1)

#Print number of differentially expressed genes.
print(enriched_result@numDE)

#Get the names of all up-regulated differentially expressed genes.
upreg_de_genes <- enriched_result@upNames
# }