analyzeAcquisitionFIA {proFIA} | R Documentation

## Wrapper function for the full FIA analysis workflow.

### Description

Perform the 4 steps pro fia workflow including :

- noise estimation. Noise is estimated.

- bands filtering. Bands are filtered using the `findFIASignal` function.

- peak grouping. Signals from different acquisition are grouped using `group.FIA` function.

- missing values imputations. Missing values are imputated using `impute.KNN_TN` function.

Minimal options to launch the workflow are provided, neithertheless if finer option tuning are necessary, launching the workflow function by function is strongly advised.

### Usage

    analyzeAcquisitionFIA(path, ppm, dmz = 0.001, fracGroup = 0.5,
      ppmGroup = NULL, dmzGroup = 5e-04, parallel = FALSE, bpparam = NULL,
      noiseEstimation = TRUE, SNT = NULL, maxo = FALSE,
      imputation = c("KNN_TN", "randomForest", "None"), ...)

### Arguments

`path` | The path to the directory of acquistion.
`ppm` | The tolerance for deviations in m/z between scan in ppm `findFIASignal`
`dmz` | The minimum tolerance for deviations in m/z between scan in Dalton `findFIASignal`
`fracGroup` | The fraction of smaple form a class necessary to make a group.
`ppmGroup` | A ppm tolerance to group signals between samples `group.FIA`.
`dmzGroup` | The minimum tolerance in Dalton to group signals between samples `group.FIA`.
`parallel` | A boolean indicating if parallelism is supposed to be used.
`bpparam` | A BiocParallelParam object to be passed i BiocParallel is used.
`noiseEstimation` | A boolean indicating in noise need to be estimated.
`SNT` | A value giving the SNT thrshold, used only if `noiseEstimation` is FALSE.
`maxo` | Should the maximum intensity be used over the peak area.
`imputation` | The method to use for imputation 'randomForest' (`impute.randomForest`) or 'KNN_TN' (`impute.KNN_TN`). Put 'None' if no imputation should be done.
`...` | Supplementary arguments to be passed to the imputation method, see `impute.FIA` for detail.

### Value

A filled proFIAset object ready for exportation.

### Examples

    if(require(plasFIA)){
        path<-system.file(package="plasFIA","mzML")

        #Defining parameters for Orbitrap fusion.
        ppm<-2
        dmz <- 0.0005
        ppm_group<-1
        dmz_group <- 0.0003
        paral<-FALSE
        frac_group<-0.2
        k<-2
        maxo<-FALSE
        vimputation <- "randomForest"
        ## Not run: plasSet<-analyzeAcquisitionFIA(path,ppm=ppm,dmz=dmz,imputation=vimputation,fracGroup=frac_group,ppmGroup=ppm_group,dmzGroup=dmz_group,k=k,maxo=maxo,parallel=paral)
    }

[Package proFIA version 1.12.0 Index]