R/trim_filt.R

In XinranMiao/Test: What the Package Does (One Line, Title Case)

#' Return Lad coefficients
#'
#' The function returns the named coefficients vector
#' @param fnFs a vector of paths for raw fastq files (forward)
#' @param filtFs a vector of paths for filtered fastq files (forward)
#' @param filtRs a vector of paths for filtered fastq files (reversed)
#' @param ... further arguments passed to or from other methods
#' @details 
#' @export
#' @examples
trim_filt <- function(fnFs, # paths for raw fastq files (forward)
                     filtFs,
                     filtRs,
                     ...){ # paths for filtered fastq files (reversed)
  for(i in seq_along(fnFs)) {
    dada2::fastqPairedFilter(c(fnFs[[i]], 
                        stringr::str_replace(fnFs[[i]],'R1','R2')#fnRs[[i]]
    ),
    c(filtFs[[i]], filtRs[[i]]),
    trimLeft=10, truncLen=c(250, 250),
    maxN=0, maxEE=2, truncQ=2,
    compress=TRUE)
  }
  return()
}