| Type: | Package |
| Title: | Aids in the Analysis of Genes Influencing Cancer Survival |
| Version: | 1.0.0 |
| Maintainer: | Pheonix Chen <shuaiyuchen4@gmail.com> |
| Description: | Aids in the analysis of genes influencing cancer survival by including a principal function, calculator(), which calculates the P-value for each provided gene under the optimal cutoff in cancer survival studies. Grounded in methodologies from significant works, this package references Therneau's 'survival' package (Therneau, 2024; https://CRAN.R-project.org/package=survival) and the survival analysis extensions by Therneau and Grambsch (2000, ISBN 0-387-98784-3). It also integrates the 'survminer' package by Kassambara et al. (2021; https://CRAN.R-project.org/package=survminer), enhancing survival curve visualizations with 'ggplot2'. |
| License: | Apache License 2.0 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.1 |
| Depends: | survival, survminer |
| NeedsCompilation: | no |
| Packaged: | 2024-03-27 04:20:49 UTC; 86157 |
| Author: | Pheonix Chen 
[aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2024-03-27 10:10:06 UTC |
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)