This is an internal function used by dnapath to conduct
the differential network analysis on a single pathway.
dna_pathway(
x,
pathway,
groups = NULL,
network_inference = run_pcor,
n_perm = 100,
lp = 2,
seed = NULL,
verbose = FALSE,
...
)The gene expression data to be analyzed. Assumed to already be
processed by dnapath
A single vector containing gene names.
A vector of length equal to the
number of rows in x containing two unique elements
(the two group names).
A function used to infer the pathway network.
The number of random permutations to perform during
permutation testing. If n_perm == 1, the permutation tests are not performed.
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).
(Optional) Used to set.seed prior to permutation test for each pathway. This allows results for individual pathways to be easily reproduced.
Set to TRUE to turn on messages.
Additional arguments are passed into the network inference function.
A list containing the results of the differential network analysis for a single pathway.