estimateNoiseMS: Estimate the noise of a mass spectrometer using multiple MS...

In proFIA: Preprocessing of FIA-HRMS data

Description

Determine the variances of the noise in function of the intensity from multiples FIA acquisitions, using the method from Wentzell and Tarazuk(2014) Characterization of heteroscedastic measurement noise in the absence of replicates

Usage

estimateNoiseMS(
  list_files,
  ppm,
  nBin = 500,
  minInt = 500,
  maxInt = 10^8,
  f = c("TIC", "regression"),
  parallel,
  includeZero = TRUE,
  dmz = 5e-04,
  BPPARAM = NULL
)

Arguments

list_files	A list of files in which the noise should be estimated.
ppm	The authorized deviation between scans in ppm, this parameter will also be used to fuse the bands if there are close enough.
nBin	The number of intensity bins to be used.
minInt	The minimum intensity expected in all the files.
maxInt	The maximum intensity expected in all the files.
f	Which method should be used to find the injection peaks. Should be 'TIC' or'regression'
parallel	Shall parrallelism be used.
includeZero	Should the left bin start a 0.
dmz	The dmz parameters to be passed to findBandsFIA, see findBandsFIA
BPPARAM	A BiocParallelParam object to be used for parallelism if parallel is TRUE.

Value

A noise estimator object.

Examples

##Listing the files in plasFIA
if(require(plasFIA)){
  list_mzml <- list.files(system.file(package="plasFIA","mzML"),full.names=TRUE)

  ##For speed purpose
  list_mzml <- list_mzml[1:2]
  es <- estimateNoiseMS(list_mzml,2,parallel=FALSE)
}

proFIA documentation built on March 20, 2021, 6 p.m.