dnapath (version 0.7.6)

dna_pathway: 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,
  ...
)

Value

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

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.