getMetDEMeta: Finds columns in differential expression table for...

In ctlab/gatom: Finding an Active Metabolic Module in Atom Transition Network

Finds columns in differential expression table for metabolites required for gatom analysis

Description

Finds columns in differential expression table for metabolites required for gatom analysis

Usage

getMetDEMeta(
  met.de.raw,
  met.db,
  idColumn = NULL,
  idType = NULL,
  pvalColumn = NULL,
  logPvalColumn = NULL,
  log2FCColumn = NULL,
  signalColumn = NULL
)

Arguments

met.de.raw	A table with differential expression results, an object convertable to data.frame.
met.db	Metabolite database
idColumn	Specifies column name with metabolite identifiers.
idType	Specifies type of metabolite IDs (one of the supported by annotation).
pvalColumn	Specifies column with p-values.
logPvalColumn	Specifies column with log p-values, if there is no such column one will be generated automatically.
log2FCColumn	Specifies column with log2-fold changes.
signalColumn	Specifies column with identifier of the measured entity Could be NULL (automatic, set from based on pval and log2FC columns), character (column name), or function (evaluated in a scope of original data frame)

Value

object with prepared columns for the analysis for metabolite data

Examples

data("met.kegg.dbEx")
data("met.de.rawEx")
de.meta <- getMetDEMeta(met.de.rawEx, met.db = met.kegg.dbEx)

ctlab/gatom documentation built on May 3, 2024, 3:44 p.m.