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

How to Use R6 Classes

Ideally I want to use R6 classes for the mzml data and peaks, so lets work out how best to actually do that.

Current Plan

AnalyzeMS

Class that controls how an analysis is run. Has methods for loading data, and peak finding (PeakFinder). The PeakFinder should be set on the generator.

PeakFinder

Takes as input two pieces from the RawMS data, the raw data and the ranges to use.

ZipMS

This is the overall data container for a zipped file of mass-spec data.

Initializer should have arguments for which peices are actually loaded, with the default being everything.

Data slots:

• metadata: a MetaData data member
• raw_ms: a RawMS data member
• peaks: a Peaks data member

Methods:

• initialize
• read
• write

RawMS

Data container for the raw mass-spec data, should take two filehandle to read in the data, one for the data, and one for metadata.

Data slots:

• metadata:
• data:
• use_scans:

Methods:

• initialize
• set_scans

library(SIRM.FTMS.peakPickingMethods)

mzml_file <- "~/Projects/work/SIRM.FTMS.automatedAssignmentProcessExampleData/UK001N1exoposb.mzML"
zip_file <- "~/Projects/work/SIRM.FTMS.automatedAssignmentProcessExampleData/UK001N1exoposb.zip"

test1 <- ZipMS$new(zip_file)

test2 <- ZipMS$new(mzml_file)

test3 <- ZipMS$new(zip_file, out_file = "crap.txt")

find_peaks_default <- function(data, scan_range){
  avg_data <- as.data.frame(xcms::getSpec(data, scanrange = scan_range))
  avg_data$ObservedMZ <- avg_data$mz
  avg_data$Intensity <- avg_data$intensity
  avg_data$mz <- NULL
  avg_data$intensity <- NULL
  avg_peaks <- find_peaks_diff(avg_data)

  function_call <- "find_peaks_diff"
  function_pkg <- find(function_call)
  pkg_desc <- utils::packageDescription(substring(function_pkg, 9))
  if (!is.null(pkg_desc$RemoteSha)) {
    pkg_sha <- pkg_desc$RemoteSha
  } else {
    pkg_sha <- ""
  }
  pkg_version <- packageVersion(substring(function_pkg, 9))
  picking_description <- list(package = function_pkg,
                             version = pkg_desc$Version,
                             sha = pkg_sha,
                             function_called = function_call,
                             parameters = list(scan_range = force(scan_range))
                             )
  PeakPickingAnalysis$new(in_peaks = avg_peaks,
                          in_parameters = list(scan_range = force(scan_range),
                                                        picking_description = picking_description))
}

anal_ms <- AnalyzeMS$new(zip_file, file.path(getwd(), "UK001N1exoposb_out.zip"))
anal_ms$load_file()

anal_ms$set_peak_finder(find_peaks)
anal_ms$find_peaks()

anal_ms$zip_ms$out_file

anal_ms$zip_ms$save()
anal_ms$zip_ms$cleanup()

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