fiveP-R

Install devtools

install.packages("devtools")

Install dependencies (to do: remove this step)

if (!requireNamespace("tidyverse", quietly = TRUE))
    install.packages("tidyverse")

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

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

# Install STRINGdb if not already installed
if (!requireNamespace("STRINGdb", quietly = TRUE)) {
  BiocManager::install("STRINGdb")
}

# Install biomaRt if not already installed
if (!requireNamespace("biomaRt", quietly = TRUE)) {
  BiocManager::install("biomaRt")
}

Install the package

devtools::install_github("martadelfino/fiveP-R")

Load the package

library(fiveP)

Example:

# Reading the file 
gene_classes <- readr::read_delim('CodeReview_data.txt', delim = '\t',  
                                      show_col_types = FALSE)

# Getting the HGNC IDs
AR <- gene_classes %>%
  dplyr::filter(ndd_ar_classes == 'positive') %>%
  dplyr::select(hgnc_id) #%>% dplyr::slice_sample(n = 5)

AR_results <- get_fiveP(AR)

print(AR_results)