Install

Installation Instructions

Prerequisites

Ensure you have R version 4.0 or above installed on your computer or server. The PCAPAM50 package relies on other R packages available from CRAN and Bioconductor.
To ensure compatibility, upgrade Bioconductor to the latest version (BiocManager v3.19).
Once R and Bioconductor are properly installed, you can proceed with the installation process.

Installing Dependencies

Dependencies: Biobase, lattice, ComplexHeatmap, and impute. You can install these packages using the following commands:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ComplexHeatmap")
BiocManager::install("impute")
BiocManager::install("Biobase")
install.packages("lattice")

Installing PCA-PAM50

To install PCA-PAM50 from CRAN, use the following command:

install.packages("PCAPAM50")

Alternatively, to install the package from a tar.gz file, use:

install.packages("PCAPAM50_1.0.0.tar.gz", repos = NULL, type = "source")

Loading PCA-PAM50 and Dependencies

After installation, load the PCAPAM50 package and the required libraries in your R session:

library("PCAPAM50")  
library("Biobase")  
library("lattice")  
library("ComplexHeatmap")  
library("impute")