hipathia {hipathia} | R Documentation

## Computes the level of activation of the subpathways for each of the samples

### Description

#@importFrom igraph

### Usage

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

### Arguments

`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.

### Value

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`.

### Examples

    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)

[Package hipathia version 2.4.0 Index]