findNeutralLossSpecs: Find pseudospectra that contains a specific neutral loss

In CAMERA: Collection of annotation related methods for mass spectrometry data

Description

The method searches in every pseudospectra for a distance between two ions matching a provided mass difference. It returns a boolean vector with the length equals to the number of pseudospectra, where a hit is marked with TRUE.

Usage

  findNeutralLossSpecs(object, mzdiff=NULL, mzabs=0, mzppm=10)

Arguments

object	xsAnnotate object
mzdiff	neutral loss in Dalton
mzabs	absolut allowed mass difference
mzppm	relative allowed mass difference

Details

The function needs a xsAnnotate object after groupCorr or groupFWHM.

Author(s)

Carsten Kuhl <[e-mail]>

Examples

  library(CAMERA)
  file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
  xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
  an   <- xsAnnotate(xs)
  an   <- groupFWHM(an)
  #Searches for Pseudspecta with water loss
  hits <- findNeutralLossSpecs(an, mzdiff=18.01, mzabs=0.01) 

CAMERA documentation built on Nov. 8, 2020, 4:59 p.m.