indicate standards — indicate_standards_contaminents • ScanCentricPeakCharacterization

Given a directory of characterized samples, attempts to determine which peaks may be standards or contaminants that should be removed after assignment.

Usage

indicate_standards_contaminents(
  zip_dir,
  file_pattern = ".zip",
  blank_pattern = "^blank",
  save_dir = NULL,
  conversion_factor = 400,
  progress = TRUE
)

Arguments

zip_dir: which directories to look for files within
file_pattern: what files are we actually using
blank_pattern: regex indicating that a sample may be a blank
save_dir: where to save the files (default is to overwrite originals)
conversion_factor: how much to multiply frequencies by
progress: should progress messages be displayed?

Value

NULL nothing is returned, files are overwritten

Details

For each sample, the scan level frequencies are read in and converted to ranges, and then compared with tiled ranges over the whole frequency range. For those ranges that have 90 to 110% of scan level peaks in ALL blanks, and have 10 to 110% of scan level peaks in at least N-sample - 1, we consider a possible standard or contaminant. The peak is marked so that it can be removed by filtering out it's assignments later.