dnapath: Differential network analysis
In tgrimes/dnapath2: Differential Network Analysis Using Gene Pathways

Differential network analysis

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dnapath(expr_pair, pathway_list, groups = NULL,
  network_inference = run_pcor, n_perm = 100, lp_set = 2,
  seed = NULL, verbose = TRUE)

`expr_pair`	Either (1) a list of two matrices, or objects to be coerced to one, that contain the gene expression profile from two populations (groups), or (2) a single matrix, or object to be coerced to one, that contains the expression profiles for both groups. In either case, the rows of each matrix should correspond to samples and the columns should correspond to individual genes. If a single matrix is provided, the `groups` argument must also be set to specify which rows belong to which group.
`pathway_list`	A single vector or list of vectors containing gene names to indicate pathway membership. The vectors are used to subset the matrices in 'expr_pair'.
`groups`	(Optional) If `expr_pair` is a single matrix, `groups` must be a vector of length equal to the number of rows in `expr_pair`, and it should contain two unique elements (for example, the two group names). This argument is used to identify which samples belong to which group.
`network_inference`	A function used to infer the pathway network. It should take in an n by p matrix and return a p by p matrix of association scores. (Built-in options include: `run_aracne`, `run_bc3net`, `runc3net`, `run_clr`, `run_corr`, `run_dwlasso`, `run_genie3`, `run_glasso`, `run_mrnet`, `run_pcor`, and `run_silence`.) Defaults to `run_pcor` for partial correlations.
`n_perm`	The number of random permutations to perform during permutation testing. If n_perm == 1, the permutation tests are not performed. If n_perm is larger than the number of possible permutations, n_perm will be set to this value with a warning message.
`lp_set`	A vector of lp values used to compute differential connectivity scores. If multiple values are given, then the results are returned as a list having the same length. (Note: the option of providing a vector of lp values is available so that network inference methods only need to be run once for each pathway).
`seed`	(Optional) Used to set.seed prior to permutation test for each pathway. This allows results for individual pathways to be easily reproduced.

A list containing results for each pathway in 'pathway_list'. These results include the p-values for differential connectivity of each gene, the overall differential connectivity of the pathway. Pathways without any significance are excluded from the results.

tgrimes/dnapath2 documentation built on May 21, 2020, 5:53 p.m.