Description Usage Arguments Details Value Examples
clust.expand
returns a list of kinase substrate relationships
1 | clust.expand(clust, clust_all, diff = NULL)
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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 |
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.
named list containing named vectors of cluster assignments, names correspond to rownames in data and names of list are kinase identifiers
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | 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)
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