normalize_paths: Normalize the pathway matrix by rows
In hipathia: HiPathia: High-throughput Pathway Analysis

Description Usage Arguments Details Value Examples

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.

1	normalize_paths(path_vals, metaginfo)

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

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.

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

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