estimateNoiseMS: Estimate the noise of a mass spectrometer using multiple MS...
In adelabriere/proFIA: Preprocessing of FIA-HRMS data

Description Usage Arguments Value Examples

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

1 2	estimateNoiseMS(list_files, ppm, nBin = 500, minInt = 500, maxInt = 10^8, parallel, includeZero = TRUE, dmz = 5e-04, BPPARAM = NULL)

`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.
`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.

A noise estimator object.

##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)
}