PIK: Pathway induced kernel (Manica et al. 2019)

In vittoriofortino84/COPS: Clustering algorithms for Omics-driven Patient Stratification

Pathway induced kernel (Manica et al. 2019)

Description

Pathway induced kernel (Manica et al. 2019)

Usage

PIK(x, L, rwr_smoothing = FALSE, rwr_restart_prob = 0.75, ...)

PIK_KEGG(x, gene_key = "SYMBOL", ...)

PIK_from_networks(x, networks, normalized_laplacian = TRUE, parallel = 1, ...)

PIK_GNGS(x, gene_network, gene_sets, ...)

Arguments

x	gene feature matrix
L	pathway graph Laplacian matrix
rwr_smoothing	apply feature smoothing
rwr_restart_prob	restart probability for smoothing
...	passed on to PIK
gene_key	column in org.Hs.eg.db that KEGG IDs should be translated to
networks	list of igraph objects corresponding to pathway graphs
normalized_laplacian	normalize Laplacian for calculations
parallel	number of parallel threads
gene_network	igraph object
gene_sets	list of gene sets

Value

kernel matrix

list of KEGG-based pathway-kernel matrices

list of kernel matrices

list of kernel matrices

Functions

• PIK_KEGG(): Use KEGG pathways to form pathway induced kernels

• PIK_from_networks(): Pathway induced kernel from networks

• PIK_GNGS(): Extract subnetworks based on pathway genesets and compute PIKs

vittoriofortino84/COPS documentation built on Jan. 28, 2025, 3:16 p.m.