R: Differential network analysis on a single pathway

dna_pathway {dnapath} | R Documentation

## Differential network analysis on a single pathway

### Description

This is an internal function used by `dnapath` to conduct the differential network analysis on a single pathway.

### Usage

    dna_pathway(
      x,
      pathway,
      group_prob,
      network_inference,
      permutations,
      lp = 2,
      verbose = FALSE,
      ...
    )

### Arguments

`x` | The gene expression data to be analyzed. Assumed to already be processed by `dnapath`
`pathway` | A single vector containing gene names.
`group_prob` | A matrix with number of rows equal to the number of rows in `x` and two columns, each containing the probability that a given observation belongs to each group.
`network_inference` | A function used to infer the pathway network.
`permutations` | A matrix containing the permutations to perform during permutation testing. If `NULL`, the permutation tests are not performed.
`lp` | The lp value used to compute differential connectivity scores. (Note: If a vector is provided, then the results are returned as a list of `dnapath_list` objects, one result for each value of `lp`. This option is available so that network inference methods only need to be run once for each pathway when multple values of `lp` are being considered. This may be useful when conducting simulation studies).
`verbose` | Set to TRUE to turn on messages.
`...` | Additional arguments are passed into the network inference function.

### Value

A list containing the results of the differential network analysis for a single pathway.

[Package dnapath version 0.7.4 Index]