R/ReadingInFastQC.R

In spirpinias/kamaki: Data Manipulation

#' Function for parsing the text output of FastQC
#'
#' This functions extracts the values for a specific test run by FastQC on a
#' single fastq file.
#'
#' @param file string that specifies the path to an individual FastQC result file
#' (tyically named "fastqc_data.txt"
#' @param test Indicate which test results should be extracted. Default:
#' "Per base sequence quality". Other options are, for example, "Per tile sequence quality",
#' "Per sequence quality score" etc.
#'
#' @return data.frame with the values of a single FastQC test result.
#'
#' @examples \dontrun{
#' res <- reading_in(file = "acinar-3_S9_L001_R1_001_fastqc/fastqc_data.txt")
#' }
reading_in <- function(file, test = "Per base sequence quality", input, input2){

  ## generate the string that will be used for the file parsing
  syscommand <- paste0("sed -n '/", test, "/,/END_MODULE/p' ", file, " | grep -v '^>>'")

  ## use the fread command, which can interpret UNIX commands on the fly to
  ## read in the correct portion of the FastQC result
  dat <- data.table::fread( cmd = syscommand, header = TRUE) %>% as.data.frame
  dat[, "Sample"] <- input
  dat[, "Genotype"] <- input2


  return(dat)

}