calculator: calculator of Pvalue

In Oncofilterfast: Aids in the Analysis of Genes Influencing Cancer Survival

calculator of Pvalue

Description

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

Usage

calculator(survival, RNA, result)

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

Value

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

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)

Oncofilterfast documentation built on May 29, 2024, 12:18 p.m.