clustering {ksrlive}

Return clustering assignments produced by tight.clust

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)