estimateNoiseMS {proFIA} | R Documentation

## Estimate the noise of a mass spectrometer using multiple MS acquisition.

### 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)
    }

[Package proFIA version 1.18.0 Index]