hipathia: Computes the level of activation of the subpathways for each...
In hipathia: HiPathia: High-throughput Pathway Analysis

Description Usage Arguments Value Examples

#@importFrom igraph

1 2	hipathia(genes_vals, metaginfo, sel_assay = 1, decompose = FALSE, maxnum = 100, verbose = TRUE, tol = 1e-06, test = TRUE)

`genes_vals`	A SummarizedExperiment or matrix with the normalized expression values of the genes. Rows represent genes and columns represent samples. Rownames() must be accepted gene IDs.
`metaginfo`	Pathways object
`sel_assay`	Character or integer, indicating the assay to be processed in the SummarizedExperiment. Only applied if `genes_vals` is a `SummarizedExperiment`.Default is 1.
`decompose`	Boolean, whether to compute the values for the decomposed subpathways. By default, effector subpathways are computed.
`maxnum`	Number of maximum iterations when iterating the signal through the loops into the pathways
`verbose`	Boolean, whether to show details about the results of the execution of hipathia
`tol`	Tolerance for the difference between two iterations when iterating the signal through the loops into the pathways
`test`	Boolean, whether to test the input objects. Default is TRUE.

A MultiAssayExperiment object with the level of activation of the subpathways from the pathways in pathigraphs for the experiment with expression values in genes_vals.

data(exp_data)
pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
"hsa04012"))
results <- hipathia(exp_data, pathways, verbose = TRUE)
## Not run: results <- hipathia(exp_data, pathways, decompose = TRUE, 
verbose = FALSE)
## End(Not run)