getGeneDEMeta: Finds columns in gene differential expression table required...

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

Finds columns in gene differential expression table required for gatom analysis

Description

Default values for all columns are NULL which mean they are determined automatically.

Usage

getGeneDEMeta(
  gene.de.raw,
  org.gatom.anno,
  idColumn = NULL,
  idType = NULL,
  pvalColumn = NULL,
  logPvalColumn = NULL,
  log2FCColumn = NULL,
  baseMeanColumn = NULL,
  signalColumn = NULL,
  signalRankColumn = NULL
)

Arguments

gene.de.raw	A table with differential expression results, an object convertable to data.frame.
org.gatom.anno	Organsim-specific annotation obtained from makeOrgGatomAnnotation function.
idColumn	Specifies column name with gene identifiers.
idType	Specifies type of gene 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.
baseMeanColumn	Specifies column with average expression across samples.
signalColumn	Specifies column with identifier of the measured entity (such as gene ID for RNA-seq and probe ID for microarrays). 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)
signalRankColumn	Specifies how the genes are ranked from highly to lowly expressed, used in 'addHighlyExpressedEdgues' function. Could be NULL (automatic), character (column name) function (evaluated in a scope of original data frame).

Value

object with prepared columns for the analysis for gene data

Examples

data("org.Mm.eg.gatom.annoEx")
data("gene.de.rawEx")
de.meta <- getGeneDEMeta(gene.de.rawEx, org.gatom.anno = org.Mm.eg.gatom.annoEx)

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