Oncofilterfast (version 1.0.0)

calculator: calculator of Pvalue

Description

By using this function, you can calculate the Pvalue of all genes you have provided.

Usage

calculator(survival, RNA, result)

Value

this function will return a dataframe that contains either the gene's ensemble IDs and it's Pvalue.

Arguments

survival

the dataframe that contains survival data

RNA

the dataframe that contains the expression data of genes

result

the dataframe which will contains the outcome

Examples

library(Oncofilterfast)
result <- data.frame(gene = c("A"),Pvalue = c(1))
RNA_all_path=system.file("extdata", "TCGA-LGG.htseq_fpkm.tsv", package = "Oncofilterfast")
RNA_all=read.csv(RNA_all_path,header=TRUE,sep="\t")
rows_to_keep <- apply(RNA_all[, -1], 1, function(row) {
  non_zero_count <- sum(row != 0)
  total_elements <- length(row)
  (non_zero_count / total_elements) >= 0.5
  })
RNA <- RNA_all[rows_to_keep, ]
survival_path=system.file("extdata", "TCGA-LGG.survival.tsv", package = "Oncofilterfast")
survival=read.csv(survival_path,header=TRUE,sep="\t")
final=calculator(survival=survival,RNA=RNA,result=result)
print(nrow(final))
filtered_result <- final[final$Pvalue < 0.01, ]
print(nrow(filtered_result))
print(filtered_result)