metaDEG: meta differential gene expression (DEG) analysis

In adamsardar/metaDEGth: Combining differential expression P-values in a statistically consistent fashion whilst respecting background signal/noise trends

meta differential gene expression (DEG) analysis

Description

Given a collection of gene sets and

Usage

metaDEG(pValueSet, geneSet, betaUniformFit, ...)

## S4 method for signature 'data.frame,data.frame,BetaUniformModel'
metaDEG(
  pValueSet,
  geneSet,
  betaUniformFit,
  pValAttr = "pVal",
  geneSetNameAttr = "geneSet",
  geneSetMembersAttr = "gene"
)

## S4 method for signature 'data.table,data.table,missing'
metaDEG(pValueSet, geneSet, betaUniformFit, pValAttr, plot = TRUE, ...)

## S4 method for signature 'ANY,list,ANY'
metaDEG(
  pValueSet,
  geneSet,
  geneSetNameAttr = "geneSet",
  geneSetMembersAttr = "gene",
  ...
)

## S4 method for signature 'numeric,ANY,ANY'
metaDEG(
  pValueSet,
  geneSet,
  pValAttr = "pVal",
  geneSetMembersAttr = "gene",
  ...
)

Arguments

pValueSet	P-values from experimental assay
geneSet	Gene set collections
betaUniformFit	A beta-uniform model of the P-value distribution - optional - can be estimated from the P-Values provided
...	Additional parameters for methods
pValAttr	The name of the P-value attribute in the pValueSet frame
geneSetNameAttr	The name of the gene set identifier attribute in the geneSet frame
geneSetMembersAttr	The name of the gene set members attribute in the geneSet frame
plot	Logical - draw a plot or not - default TRUE

Value

A frame of gene sets, their members, their sizes and their meta-analysis P-values

Functions

• metaDEG,data.frame,data.frame,BetaUniformModel-method: Build a beta-uniform model on the fly

• metaDEG,data.table,data.table,missing-method: Build a betaUniform model on the fly

• metaDEG,ANY,list,ANY-method: Provide geneSet as a named list of members

• metaDEG,numeric,ANY,ANY-method: Provide pValueSet as a uniquely named numeric vector of pvalues

adamsardar/metaDEGth documentation built on Sept. 28, 2022, 10:12 p.m.