netDEG {Corbi}

netDEG: Differentially expressed gene identification method

Description

Perform netDEG for two group samples.

Usage

netDEG(
  ref.expr.matrix,
  expr.matrix,
  p.edge = 0.1,
  summarize = c("gene", "sample"),
  summarize.method = c("sumlog", "sumlog"),
  summarize.shrink = c(Inf, Inf),
  log.expr = FALSE,
  zero.as.dropout = TRUE,
  scale.degree = TRUE,
  use.parallel = FALSE
)

Arguments

ref.expr.matrix

The reference expression matrix. Each row represents a gene and each column represents a sample.

expr.matrix

The test expression matrix. Each row represents a gene and each column represents a sample.

p.edge

The expected probability of edges in the expression ratio network for a normal sample.

summarize

Character vector indicating how to summarize the results. Available methods are c("gene", "sample").

summarize.method

Character vector indicating the methods used to summarize the results. See p_combine.

summarize.shrink

Numeric vector indicating the shrink parameter to summarize the results. See p_combine.

log.expr

Logical variable indicating whether the input expression matrix is in logarithmic scale.

zero.as.dropout

Logical variable indicating whether the zero expressions are regarded as dropouts.

scale.degree

Logical variable indicating whether the degree values are scaled according to the dropout rate.

use.parallel

Logical variable indicating to use the BiocParallel package to accelerate computation.

Value

This function will return a list with the following components:

up

A numeric matrix with same dimension as expr.matrix, containing the p-values of up-regulation test.

down

A numeric matrix with same dimension as expr.matrix, containing the p-values of down-regulation test.

twoside

A numeric matrix with same dimension as expr.matrix, containing the p-values of twoside test.

rev

A list containing the reverse comparison results, containing three components: up, down, and twoside. Available if the gene method is specified in summarize argument.

gene

A list containing the gene-wise summaried results, containing three components: up, down, and twoside. Available if the gene method is specified in summarize argument.

sample

A list containing the sample-wise summaried results, containing three components: up, down, and twoside. Available if the sample method is specified in summarize argument.