R/rmSpaceInBeginning.R

In ELELAB/lipidQ: Lipidomics Analysis Tool

#' @title Remove Space In Beginning of NAME and SPECIE Rows
#' @author André Vidas Olsen
#' @description Auxiliary function that removes the first letter in NAME and
#' SPECIE, if the word begins with a [SPACE]. It is used since, by experience,
#' some rows begins with a space for these two columns which can results in
#' errors.
#' @param data data formatted by the use of the mergeDataSet function from
#' LipidQ.
#' @param userSpecifiedColnames the column names template file containing user
#' specified column names for the input data. This file
#' @return data set
rmSpaceInBeginning <- function(data, userSpecifiedColnames = NULL){

  # get colnames for data
  dataColnames <- checkColnames(userSpecifiedColnames)

  test_SUM_and_SPECIE_COMPOSITION_exists <- tryCatch(
    {

      data[,dataColnames$SUM_COMPOSITION]
      data[,dataColnames$SPECIE_COMPOSITION]

    },
    error=function(cond){
      message(paste0("ERROR: PROBLEMS WITH COLUMN NAMES! Please check that ",
        dataColnames$SUM_COMPOSITION, " and ", dataColnames$SPECIE_COMPOSITION,
        " exists in all input data sets"))
      message("")
      message("")
      message("")
      message("Original R error message:")
      message(cond)
    }
  )

  # for each row, check if either the NAME or SPECIE column begins with a
  # [SPACE] and remove this [SPACE] if true.
  data[,dataColnames$SUM_COMPOSITION] <- ifelse(substring(data[,
      dataColnames$SUM_COMPOSITION],1,1) == " ", substring(data[,
      dataColnames$SUM_COMPOSITION], 2), data[, dataColnames$SUM_COMPOSITION])

  data[, dataColnames$SPECIE_COMPOSITION] <-
    ifelse(substring(data[, dataColnames$SPECIE_COMPOSITION],1,1) == " ",
    substring(data[, dataColnames$SPECIE_COMPOSITION], 2),
    data[, dataColnames$SPECIE_COMPOSITION])


  return(data)
}