#' commonly_mut_genes
#'
#' Find genes that are commonly mutated from ClusterDF
#'
#'
#' @param ClusterDF ClusterDF
#' @export
#' @return Table with which genes in which cluster
#' @import kableExtra
#' @import dplyr
#'
#' @examples commonly_mut_genes(ClusterDF)
commonly_mut_genes <- function(ClusterDF){
setwd(main_wd)
load("MC3_ext.rda")
genes <- read.table("gen_lista.csv",header=TRUE,sep=";")
genes <- as.character(genes$Gen)
table_to_print <- tibble()
for (i in 1:length(unique(ClusterDF$cluster))){
cluster_x <- ClusterDF %>% filter(cluster == i)
cluster_MC3 <- MC3 %>% filter(Tumor_Sample_Barcode %in% cluster_x$TCGA_code)
common_mutations <- cluster_MC3 %>% dplyr::count(Hugo_Symbol,Chromosome,
Start_Position,End_Position,
Variant_Classification,HGVSp_Short)
common_mutations <- common_mutations[order(common_mutations$n,decreasing = TRUE),]
test <- head(common_mutations,30)
test <- test %>% select(n,Hugo_Symbol,HGVSp_Short,Variant_Classification)
#Check if any of the commonly mutated genes are in the genes-list
high_mut_gene <- intersect(test$Hugo_Symbol,genes)
test <- test %>% filter(Hugo_Symbol %in% high_mut_gene)
test$cluster <- c(rep(i,nrow(test)))
table_to_print <- rbind(table_to_print,test)
}
library(kableExtra)
print(formattable(table_to_print,align="l"))
return(table_to_print)
}
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