bioconductor-ptairms

name

bioconductor-ptairms

description

This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and qua

ptairMS

Workflows

Standard Workflow

Preprocess a directory of raw PTR-TOF-MS HDF5 files to calibrate, detect peaks, align samples, impute missing values, annotate VOCs, and export an ExpressionSet.

library(ptairMS)
dirRaw <- system.file("extdata/exhaledAir", package = "ptairData")

# Create ptrSet
exhaledPtrset <- createPtrSet(
  dir = dirRaw, 
  setName = "exhaledPtrset", 
  mzCalibRef = c(21.022, 60.0525), 
  fracMaxTIC =  
  saveDir  



exhaledPtrset  detectPeakexhaledPtrset


exhaledEset  alignSamplesexhaledPtrset group   fracGroup   fracExp  


exhaledEset  ptairMSimputeexhaledEset exhaledPtrset


exhaledEset  annotateVOCexhaledEset


writeEsetexhaledEset dirC  file.pathgetwd