enrich_module: show the enrichment for ontology terms for both sampleSets...

In onertipaday/rcompass: R Client for the COMPASS GrapgQL API

Description

show the enrichment for ontology terms for both sampleSets and biofeatures

Usage

enrich_module(compendium = "vespucci", module = NULL, normalization = "limma")

Arguments

compendium	A string - the selected compendium
module	A matrix or SummarizedExperiment with valid rownames (biofeatureNames) and colnames (samplesetsNames)
normalization	A string - either 'limma' (default),'tpm' or legacy as normalization

Value

a list with two data.frame (PlantOntology and GeneOntology)

Examples

## Not run: 
gene_names <- c('VIT_00s0246g00220','VIT_00s0332g00060','VIT_00s0332g00110',
'VIT_00s0332g00160','VIT_00s0396g00010','VIT_00s0505g00030','VIT_00s0505g00060'
,'VIT_00s0873g00020','VIT_00s0904g00010')
module_1 <- create_module(biofeaturesNames=gene_names, normalization = "limma")
enrich_module(module = module_1, normalization = "limma")

## End(Not run)

onertipaday/rcompass documentation built on Sept. 18, 2021, 5:13 p.m.