R: netDEG: Differentially expressed gene identification method

netDEG {Corbi} | R Documentation

## 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.

[Package Corbi version 0.6-1 Index]