vignettes/Search_ontology.R

In csetraynor/iclust2prog: Prognostic modeling of IntClust-2 (iclust2prog)

##### Relaxed Cox
devtools::document()
library(iclust2prog)
library(glmnet)
data("ic2dat")
data("iclust2_glmnet")

iclust2_features <- extract_features(iclust2_glmnet)
iclust2_features$feature <- my_replace(iclust2_features$feature)
colnames(ic2dat) <- my_replace(colnames(ic2dat))

X <- ic2dat[, iclust2_features$feature]
relaxed_enet_fit <- suppressWarnings(coxph(Surv(ic2dat$time, ic2dat$status) ~
                                             ., data = X, init = iclust2_features$coef, control = coxph.control(iter.max = 5)))


CoxTab <- par.table(relaxed_enet_fit)
require(stargazer)
stargazer(CoxTab, type = "latex", summary = FALSE, digits.extra = 3, digits = 3,
          digit.separator = ".", rownames = F)


genedata <- data.frame(Hugo_Symbol = CoxTab$Parameter, coef = CoxTab$HR)
if ("age_std" %in% genedata$Hugo_Symbol) {
  geneTable <- genedata[(-match(c("age_std", "npi"), genedata$Hugo_Symbol)),
                        ]
} else {
  geneTable <- genedata
}
geneTable <- int_coeff_tab %>% dplyr::rename(Hugo_Symbol = model)
geneTable$Hugo_Symbol_cna <- as.character(geneTable$Hugo_Symbol)
geneTable$Hugo_Symbol <- gsub("_cna.*", "", geneTable$Hugo_Symbol_cna)


# Load data target names ---------------------------- IMPORTANT : for
# this function to work the working directory has to be set
# ~/R/libs/iclust2prog
data("target_names")

geneTable$Entrez_Gene_Id <- target_names$Entrez_Gene_Id[match(geneTable$Hugo_Symbol,
                                                              target_names$Hugo_Symbol)]
geneTable

geneList <- geneTable[!is.na(geneTable$Entrez_Gene_Id), ]$HR
names(geneList) <- geneTable[!is.na(geneTable$Entrez_Gene_Id), ]$Entrez_Gene_Id
geneList

ontology_search(ont = "c1", gene_list = geneTable)
ontology_search(ont = "c2", gene_list = geneTable)
ontology_search(ont = "c3", gene_list = geneTable)
ontology_search(ont = "c4", gene_list = geneTable)  #cancer modules
ontology_search(ont = "c5", gene_list = geneTable)  #gene ontology gene set
ontology_search(ont = "c6", gene_list = geneTable)  #oncogenic signatures
ontology_search(ont = "H", gene_list = geneTable)

oncosig <- ontology_search(ont = "c6", gene_list = geneTable)
kras <- net_gene(oncosig = oncosig, path = "KRAS")
kras <- geneTable$Hugo_Symbol_cna[match(kras, geneTable$Entrez_Gene_Id)]
lef1 <- net_gene(oncosig = oncosig, path = "LEF1")
lef1 <- geneTable$Hugo_Symbol_cna[match(lef1, geneTable$Entrez_Gene_Id)]
net_gene(oncosig = oncosig, path = "MTOR")


#Optional Check other Hugo Symbol synonims in databases
gene <-  geneTable$Entrez_Gene_Id
source("https://bioconductor.org/biocLite.R")
biocLite(c("clusterProfiler","org.Hs.eg.db"))

library(clusterProfiler)
library(org.Hs.eg.db)

gene.df <- clusterProfiler::bitr(gene, fromType = "ENTREZID", toType = c("ENSEMBL",
                                                                         "SYMBOL"), OrgDb = org.Hs.eg.db)
gene.df