normalize_paths: Normalize the pathway matrix by rows

In martahidalgo/hipathia: HiPathia: High-throughput Pathway Analysis

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)

martahidalgo/hipathia documentation built on Jan. 12, 2023, 1:44 p.m.