peakMonitor: xcms results peak monitor and shiny application

In WMBEdmands/simExTargId: Simultaneous peak-picking and MS2 target identification using XCMS.

Description

xcms results peak monitor and shiny application

Usage

peakMonitor(xcmsOutput = NULL, obsNames = NULL, metab = NULL,
  qcNames = NULL, ppm = 10, rtdev = 30, maxSignalAtt = 20,
  percBelow = 20, obsTypeStr = rep("unknown_obsType", length(obsNames)),
  obsTypeCol = rep("darkgrey", length(obsNames)), launchApp = TRUE,
  analysisDir = NULL)

Arguments

xcmsOutput	character or data.frame. Full path to xcms results file (or an XCMS output file peak table in the form of a data.frame) if argument is not supplied a tcltk window will open.
obsNames	character vector of sample/QC/Blank names to identify these columns in the xcms output table. The obsNames argument should be pre-sorted in to the acquisition run order.
metab	character or data.frame. Full path to a csv file of a list of metabolites you wish to monitor (or a data.frame) if argument is not supplied a tcltk window will open. This list will be used to identify peak groups in the xcms output table within user defined ppm mass accuracy and retention time deviation parameters. The table must consist of the following 3 columns minimum name – unique name of compound mzmed – expected mass-to-charge ratio rtmed – expected retention time (in seconds)
qcNames	character vector of analytical replicate local QC names to identify these columns in the xcms output table. The qcNames argument should be pre-sorted in to the acquisition run order. These identificatory sample names are critical for CV% calculation for example.
ppm	numeric ppm mass accuracy for matching monitored metabolites to the xcms output table (default = 10 ppm).
rtdev	numeric maximum deviation in seconds for matching monitored metabolite list and the xcms output table peak groups (default = 30 seconds).
maxSignalAtt	numeric percentage (i.e. values between 0-100%, default=20%) maximum percentage last quality control signal attenuation from the quality controls median value. If a monitored metabolite drops below this value then (i.e. -20%) then it will be flagged in the returned table.
obsTypeStr	character vector equal in length to obsNames to identify different run types in the obsNames argument.
obsTypeCol	character vector colours equal in length to obsNames to display for run types in application.
launchApp	logical default is true. If true peakMonitor shiny app will open in your default web browser.
analysisDir	the full path of the peakMonitor directory (output/peakMonitor) containing the output files (.csv) from peakMonitor. This argument is only required if the argument launchApp is TRUE. If the argument is not supplied but required then a tcltk window will open and the directory can be selected.
maxBelow	numeric (values between 0-100%, default = 20 %) maximum percentage of monitored metabolites below the maximum signal attenutation argument (see argument maxSignalAtt). E.g. if 20% of monitored metabolites contained in expected metabolite table have dropped below 20% median QC signal signal attenuation.

Value

a list containing two elements named:

1. "monitMetab" a data.frame containing the metabolite peak monitoring results.

2. "percBelow" a logical whether the user parameterized maximum percentage of monitored metabolites were below the maximum signal attenuation value. This value is used by simExTargId to notify the user of any significant signal attenuation drop during a run for example.

WMBEdmands/simExTargId documentation built on May 24, 2019, 2:08 a.m.