R/log2_norm.R

In hirscheylab/proteins: Proteins Data Sets and Utility Functions

#' Log2 normalization of proteomic data
#'
#' @description Log2 normalizes your proteomic data
#'
#' @param data The dataframe that you want to normalize, with all of the samples you want to normalize in the last columns
#' @param num_sample The number of samples in your dataframe that your are normalizing
#'
#' @return data_log2_normalized The log2 normalized data
#'
#' @export
#'

log2_normalize <- function(data, num_sample){
  # Initialize data structures and calculate the Log2 abundances
  head <- select(data, (1:(ncol(data) - num_sample)))
  data <- bind_cols(select(data, "unique_id"),
                    select(data, tail(1:ncol(data), num_sample)))
  data_log2 <- log2(data[2:ncol(data)])
  names(data_log2) <- paste("LOG2 ", names(data_log2))

  # Calculate the average of the Log2 abundances
  data_log2$LOG2_AVG <- rowMeans(select(data_log2, grep("LOG2 ", names(data_log2))))

  # Calculate the Log2 normalization of the abundances (Log2 Abundance - Log2 Average)
  data_log2_normalized <- select(data_log2, grep("LOG2 ", names(data_log2))) - data_log2$LOG2_AVG
  names(data_log2_normalized) <- gsub("LOG2", "Log2 Normalized", names(data_log2_normalized))
  data_log2_normalized <- bind_cols(select(data, "unique_id"),
                                    data_log2_normalized)
  data_log2_normalized <- left_join(head, data_log2_normalized, by = "unique_id")
  return(data_log2_normalized)
}