In janbrederecke/prepareD: Functions that help to prepare data before analysis

knitr::opts_chunk$set(echo = TRUE)

Step 0: Loading packages and annotation file

# Recording time 
prepareD::time_start()

# Loading R packages 
library(here)
library(prepareD)

# Reading annotation file 
documents_folder <- paste0(here(),"/documents/annotation/")
annotation <- read.csv(paste0(documents_folder, "/annotation.csv"),
                              stringsAsFactors = FALSE)
annotation[[1]] <- tolower(annotation[[1]]) 
rownames(annotation) <- annotation[[1]]

# Loading additional functions not available in packages
source(here("R/01-data-processing/00_functions.R"))

Step 1: Loading data

# You might want to use this to speed up the initial loading of data
data_folder <- paste0(here(),"/data/raw/")
data <-
  data.table::fread(
    paste0(data_folder, "YOURDATA.csv"),
    stringsAsFactors = FALSE,
    check.names = TRUE,
    data.table = FALSE
  )

Saving processed data

# System info
system_info <- Sys.info()  

# Saving results
to_save <- c("data"
             , "annotation")
file <- paste0(here(), "/data/cleaned/read_data.RData")
to_save <- c(to_save
             , system_info)
save(list = to_save,
     file = file)

R session information

This file was created on r date() with r R.Version()$version.string.

time_stop()

It took r time_it_took for all analyses to run.

sessionInfo()
rm(list = ls())

janbrederecke/prepareD documentation built on Oct. 26, 2022, 8:06 p.m.