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+++ b/Univariate_Multivariate_analysis.Rmd
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+---
+title: "Univariate_Multivariate"
+author: "Pranjal Vaidya"
+date: "`r Sys.Date()`"
+linkcolor: blue
+output:
+  rmdformats::readthedown:
+    highlight: kate
+    number_sections: true
+    code_folding: show
+---
+
+# Introduction 
+
+Generating Radiomic Signature for predicting Disease-Free Survival in Early-Stage NSCLC.
+
+# Data Load/Merge
+
+Initial Setup and Package Loads in R 
+
+Packages used for the analysis.
+```{r initial_setup, cache=FALSE, message = FALSE, warning = FALSE}
+library(glmnet);library(survival);library(survminer);library(readxl);library(ggplot2); library(GGally);library(knitr); library(rmdformats); library(magrittr);
+library(skimr); library(Hmisc); library(Epi); library(vcd); library(tidyverse) 
+
+source("Love-boost.R")
+
+## Global options
+
+options(max.print="75")
+opts_chunk$set(comment=NA,
+               message=FALSE,
+               warning=FALSE)
+opts_knit$set(width=75)
+
+
+skimr::skim_with(numeric = list(hist = NULL),
+                 integer = list(hist = NULL))
+```
+
+## Loading the Raw Data into R 
+
+Loading raw dataset into R.
+
+Training Data from CCF with minimum and max. survival time.
+```{r}
+train1 <- read.csv("dataset_train.csv")
+train <- na.omit(train1)
+train %>%
+  select(QuRiS) %>%
+  summary()
+```
+
+```{r}
+variables <- c( "stage", "feature22")
+formula <- sapply(variables,
+                        function(x) as.formula(paste('Surv(time, status)~', x)))
+
+univariate_analysis <- lapply(formula, function(x){coxph(x, data = train)})
+# Extract data 
+results <- lapply(univariate_analysis,
+                       function(x){ 
+                         x <- summary(x)
+                         p.value<-signif(x$wald["pvalue"], digits=4)
+                         beta<-signif(x$coef[1], digits=4);#coeficient beta
+                         HR <-signif(x$coef[2], digits=4);#exp(beta)
+                         HR.confint.lower <- signif(x$conf.int[,"lower .95"], 2)
+                         HR.confint.upper <- signif(x$conf.int[,"upper .95"],2)
+                         HR <- paste0(HR, " (", 
+                                      HR.confint.lower, "-", HR.confint.upper, ")")
+                         res<-c(beta, HR, p.value)
+                         names(res)<-c("beta", "HR (95% CI for HR)", 
+                                       "p.value")
+                         return(res)
+                       })
+res <- t(as.data.frame(results, check.names = FALSE))
+as.data.frame(res)
+```
+
+
+
+