clust.expand {ksrlive}

Find clusters containing core substrates

Description

clust.expand returns a list of kinase substrate relationships

Usage

clust.expand(clust, clust_all, diff = NULL)

Arguments

clust

named list containing named vectors of cluster assignments, names correspond to rownames in data and names of list are kinase identifiers (result of clustering performed using exclusive substrates)

clust_all

named list containing named vectors of cluster assignments, names correspond to rownames in data and names of list are kinase identifiers (result of clustering performed using all substrates)

diff

character vector of substrate identifiers that are differentially regulated

Details

The function clust.expand takes the resulting core substrates from the exclusive clustering and finds the corresponding substrate clusters in the clustering using all 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)
                        
# do clustering using all available substrates
kin_data_fam <- KSR.list(phosphonetwork_data[, c("SUB_IDENT", "KIN_ACC_ID")], 
                         kinasefamilies = fam)

substrate_profiles_all <- lapply(kin_data_fam[c("P31749", "P42345")], 
function(x){data_kin[match(x, data_kin[,"SUB_IDENT"]),1:9]})

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

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

kin_clust_all <- mapply(function(x,y){clustering(x, y)}, 
                        substrate_profiles_tight_all, substrate_profiles_all, 
                        SIMPLIFY = FALSE)
                        
expand_all <- mapply(function(x,y){clust.expand(x, y)}, 
                        kin_clust, kin_clust_all, SIMPLIFY = FALSE)