analyzeAcquisitionFIA: Wrapper function for the full FIA analysis workflow.
In adelabriere/proFIA: Preprocessing of FIA-HRMS data

Description Usage Arguments Value Examples

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.

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"), ...)

`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.

A filled proFIAset object ready for exportation.

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)
}