dna_pathway: Differential network analysis on a single pathway
In dnapath: Differential Network Analysis using Gene Pathways

dna_pathway

R Documentation

Differential network analysis on a single pathway

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

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

`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.