README.md

In vijaykumarmuley/findPvalueCutoff: Select Differentially Expressed Genes At False Positive Rate Less Than Five Percent

findPvalueCutoff

P-value Cutoff Estimation to Select Differentially Expressed Genes

findPvalueCutoff is a R package, intended to use with uncorrected p-values obtained from differential gene expression analysis to estimate the accurate p-value threshold to select differentially expressed genes. This data-driven approach avoids using arbitrary cutoff of 0.05 p-value, and particularly useful when thousands of genes appear differentially expressed when sample sizes are large.

Installation

Few R packages are required to install findPvalueCutoff. These can be installed by executing following chunk of code in R. In principle, only devtools package is required to install findPvalueCutoff. But other packages build ready to use documentation about running and working with findPvalueCutoff. For Windows operating system, RTools software should be already installed. Windows users can download and install RTools from here.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
if (!requireNamespace("BiocStyle", quietly = TRUE))
    BiocManager::install("BiocStyle")
if (!requireNamespace("knitr", quietly = TRUE))
    install.packages("knitr")
if (!requireNamespace("rmarkdown", quietly = TRUE))
    install.packages("rmarkdown")
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

Then, copy and paste following command in R console to Install findPvalueCutoff

devtools::install_github("vijaykumarmuley/findPvalueCutoff", build_vignettes = TRUE)

In case having trouble, try running above command by setting build_vignettes to FALSE.

Load findPvalueCutoff into your R workspace using following command after its installation.

library(findPvalueCutoff)

Browse findPvalueCutoff documentation using following command. It has details on how to use findPvalueCutoff with demonstrated examples, and also theoretical background behind it.

browseVignettes("findPvalueCutoff")

Contact

For questions regarding findPvalueCutoff, contact the author at vijay.muley\@gmail.com

vijaykumarmuley/findPvalueCutoff documentation built on Dec. 23, 2021, 3:11 p.m.