constructHetNet: Construct Heterogeneous network

In JoWatson2011/phosphoRWHN: Random Walk on Heterogeneous Network For Functional Analysis of Phosphoproteomics Data

Description

Construct Heterogeneous network

Usage

constructHetNet(
  clustering,
  phosphoData = NULL,
  enrichrLib = "GO_Biological_Process_2018",
  stringConf = c(0.4, 0.7),
  modules = T,
  pval = 0.05,
  simplify = T
)

Arguments

clustering	A named vector; names correspond to sites in format Gene name_AminoAcid+Position (e.g. MAPK1_T185), values correspond to cluster
phosphoData	Optional; data frame with IDs in format Gene name_AminoAcid+Position (e.g. MAPK1_T185) in column 1, quantitative values in subsequent columns
enrichrLib	Library to extract functional annotations on. See https://maayanlab.cloud/Enrichr/#stats
stringConf	numeric; value between 0 and 1, definining confidence of STRING interactions for the formation of the protein layer
modules	Calculate enrichment based on modules ? otherwise will be calculated on clusters
pval	Integer; enrichment cut-off. Default 0.05
simplify	Logical; if enrichR library is GO_Biological_Process_2018 or KEGG pathway, slim list of functional annotations?

Value

A list containing edgelists and vertices of heterogeneous network

Examples

cl <- c("MAPK1_T185" = 1, "MAPK3_T202" = 1,
        "RAF1_S338" = 2, "RAF1_T491" = 2)
constructHetNet(cl)

JoWatson2011/phosphoRWHN documentation built on Jan. 28, 2022, 4:02 a.m.