normalize_paths {hipathia} | R Documentation

## Normalize the pathway matrix by rows

### Description

Due to the nature of the Hipathia method, the length of a pathway may influence its signal rank. In order to compare signal values among subpathways, we strongly recommend to normalize the matrix with this normalization.

### Usage

    normalize_paths(path_vals, metaginfo)

### Arguments

`path_vals` | SummarizedExperiment or matrix of the pathway values
`metaginfo` | Pathways object

### Details

This function removes the bias caused by the length of the subpathways by dividing by the value obtained from running the method with a basal value of 0.5 at each node.

### Value

SummarizedExperiment or matrix of normalized pathway values, depending on the class of `path_vals`.

### Examples

    data(path_vals)
    pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
    "hsa04012"))
    path_normalized <- normalize_paths(path_vals, pathways)

[Package hipathia version 2.10.0 Index]