cpdbEnrichmentAnalysis: CPDB Enrichment Analysis
In isglobal-brge/brgeEnrich: Enrichment

Description Usage Arguments Value Examples

View source: R/cpdbEnrichmentAnalysis.R

Performs Wilcoxon enrichment analysis of functional sets with provided physical entities from CPDB.

cpdbEnrichmentAnalysis(
  entityType,
  accNumbers,
  mv1,
  mv2 = NULL,
  accType,
  fsetType,
  pThreshold = 1
)

`entityType,`	should be either 'genes' or 'metabolites'.
`accNumbers`	is a list of interesting accNumbers (e.g. differentially expressed)
`mv1`	is a list of mesured value 1 or fold change if m2 is null
`mv2`	is a list of mesured value 2
`accType`	is a valid accession number type.
`fsetType,`	the type of the functional sets to be tested (as obtained with the getCpdbAvailableFsetTypes function; e.g. 'P' for pathways).
`pThreshold,`	a p-value threshold, only sets with significant enrichment below or equal to this threshold will be provided.

cpdbIds, mapped accession numbers

library(PathData)

accType <- "uniprot"
accNumbers <- c("MDHM_HUMAN", "MDHC_HUMAN", "DLDH_HUMAN", "DHSA_HUMAN", "DHSB_HUMAN", "C560_HUMAN", "DHSD_HUMAN", "ODO2_HUMAN", "ODO1_HUMAN", "CISY_HUMAN", "ACON_HUMAN", "IDH3A_HUMAN", "IDH3B_HUMAN", "IDH3G_HUMAN", "SUCA_HUMAN", "SUCB1_HUMAN", "FUMH_HUMAN", "OGDHL_HUMAN", "ACOC_HUMAN", "DHTK1_HUMAN", "AMAC1_HUMAN")

mv1 <- runif(length(accNumbers))
mv2 <- runif(length(accNumbers))

eanalysis <- cpdbEnrichmentAnalysis("genes", accNumbers, mv1, mv2, "uniprot", "C", 1)