manualChromPeaks: Manual peak integration and feature definition

In sneumann/xcms: LC-MS and GC-MS Data Analysis

Manual peak integration and feature definition

Description

The manualChromPeaks function allows to manually define chromatographic peaks, integrate the intensities within the specified peak area and add them to the object's chromPeaks matrix. A peak is not added for a sample if no signal was found in the respective data file.

Because chromatographic peaks are added to eventually previously identified peaks, it is suggested to run refineChromPeaks() with the MergeNeighboringPeaksParam() approach to merge potentially overlapping peaks.

The manualFeatures function allows to manually group identified chromatographic peaks into features by providing their index in the object's chromPeaks matrix.

Usage

manualChromPeaks(object, ...)

manualFeatures(object, ...)

## S4 method for signature 'MsExperiment'
manualChromPeaks(
  object,
  chromPeaks = matrix(numeric()),
  samples = seq_along(object),
  msLevel = 1L,
  chunkSize = 2L,
  BPPARAM = bpparam()
)

## S4 method for signature 'XcmsExperiment'
manualChromPeaks(
  object,
  chromPeaks = matrix(numeric()),
  samples = seq_along(object),
  msLevel = 1L,
  chunkSize = 2L,
  BPPARAM = bpparam()
)

## S4 method for signature 'XcmsExperiment'
manualFeatures(object, peakIdx = list(), msLevel = 1L)

## S4 method for signature 'OnDiskMSnExp'
manualChromPeaks(
  object,
  chromPeaks = matrix(),
  samples = seq_along(fileNames(object)),
  msLevel = 1L,
  BPPARAM = bpparam()
)

## S4 method for signature 'XCMSnExp'
manualChromPeaks(
  object,
  chromPeaks = matrix(),
  samples = seq_along(fileNames(object)),
  msLevel = 1L,
  BPPARAM = bpparam()
)

## S4 method for signature 'XCMSnExp'
manualFeatures(object, peakIdx = list(), msLevel = 1L)

Arguments

object	XcmsExperiment, XCMSnExp or OnDiskMSnExp object.
...	ignored.
chromPeaks	For manualChromPeaks: matrix defining the boundaries of the chromatographic peaks with one row per chromatographic peak and columns "mzmin", "mzmax", "rtmin" and "rtmax" defining the m/z and retention time region of each peak.
samples	For manualChromPeaks: optional integer defining individual samples in which the peak integration should be performed. Defaults to all samples.
msLevel	integer(1) defining the MS level in which peak integration should be performed. Only a single MS level at a time is supported. Defaults to msLevel = 1L.
chunkSize	integer(1) defining the number of files (samples) that should be loaded into memory and processed at the same time. Peak integration is then performed in parallel (per sample) on this subset data. This setting thus allows to balance between memory demand and speed (due to parallel processing). Because parallel processing can only performed on the subset of data currently loaded into memory in each iteration, the value for chunkSize should match the defined parallel setting setup. Using a parallel processing setup using 4 CPUs (separate processes) but using ⁠chunkSize = ⁠1⁠will not perform any parallel processing, as only the data from one sample is loaded in memory at a time. On the other hand, setting⁠chunkSize' to the total number of samples in an experiment will load the full MS data into memory and will thus in most settings cause an out-of-memory error.
BPPARAM	parallel processing settings (see bpparam() for details).
peakIdx	For manualFeatures: list of integer vectors with the indices of chromatographic peaks in the object's chromPeaks matrix that should be grouped into features.

Value

XcmsExperiment or XCMSnExp with the manually added chromatographic peaks or features.

Author(s)

Johannes Rainer

Examples

## Read a test dataset.
fls <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
         system.file("microtofq/MM8.mzML", package = "msdata"))

## Define a data frame with some sample annotations
ann <- data.frame(
    injection_index = 1:2,
    sample_id = c("MM14", "MM8"))

## Import the data
library(MsExperiment)
mse <- readMsExperiment(fls)

## Define some arbitrary peak areas
pks <- cbind(
    mzmin = c(512, 234.3), mzmax = c(513, 235),
    rtmin = c(10, 33), rtmax = c(19, 50)
)
pks

res <- manualChromPeaks(mse, pks)
chromPeaks(res)

## Peaks were only found in the second file.

sneumann/xcms documentation built on Nov. 23, 2024, 6:53 p.m.