indicate_standards_contaminents: indicate standards

In MoseleyBioinformaticsLab/FTMS.peakCharacterization: Functionality for Detecting and Characterizing Peaks

indicate standards

Description

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
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?

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.

Value

NULL nothing is returned, files are overwritten

MoseleyBioinformaticsLab/FTMS.peakCharacterization documentation built on April 27, 2022, 3:32 a.m.