clustering: Return clustering assignments produced by tight.clust

In ksrlive: Identify Kinase Substrate Relationships Using Dynamic Data

Description

clustering returns vectors of clustering assignments

Usage

clustering(tightclust, data)

Arguments

tightclust	list of objects returned by the tight.clust function
data	data frame of time course of substrates, each substrate is a row

Details

The function clustering creates a named list of cluster assignments for substrates.

Value

named list containing named vectors of cluster assignments, names correspond to rownames in data and names of list are kinase identifiers

Examples

data(phosphonetworkdf)
data(datakin)
# only need what is present in data
phosphonetwork_data <- phosphonetwork_df[
phosphonetwork_df[,"SUB_IDENT"] %in% data_kin[,"SUB_IDENT"]
,]
fam <- list(akt = c("P31749", "P31751"))
kin_data_fam_exc <- KSR.list(phosphonetwork_data[, c("SUB_IDENT", "KIN_ACC_ID")], 
                             kinasefamilies = fam,
                             exclusive = TRUE)
# only do for Akt and Mtor (P31749, P42345)
substrate_profiles <- lapply(kin_data_fam_exc[c("P31749", "P42345")], 
function(x){data_kin[match(x, data_kin[,"SUB_IDENT"]),1:9]})

substrate_profiles_random <- lapply(substrate_profiles, 
function(x){rbind(x, random.data(x, random.seed = 123))})

target <- 3
substrate_profiles_tight <- lapply(substrate_profiles_random, function(x){
tightClust::tight.clust(x, target = target, k.min = 7, resamp.num = 100, random.seed = 12345)
})

kin_clust<- mapply(function(x,y){clustering(x, y)}, 
                        substrate_profiles_tight, substrate_profiles, SIMPLIFY = FALSE)

ksrlive documentation built on May 2, 2019, 10:15 a.m.