proFIAset {proFIA} | R Documentation

## Process FIA experiment.

### Description

Processes an experiment ordered as a tree of files, and return a proFIAset object. TO check the funirshed structure you may use the `acquisitionDirectory` function.

### Usage

    proFIAset(
      path,
      ppm,
      parallel = TRUE,
      BPPARAM = NULL,
      noiseEstimation = TRUE,
      f = c("regression", "TIC"),
      graphical = FALSE,
      ...
    )

### Arguments

`path` | The path of the files to be processed.
`ppm` | The tolerance of the algorithms in deviation between scans.
`parallel` | Shall parallelism using BiocParallel be used.
`BPPARAM` | A BiocParallelParam object to be used for parallelism if parallel is TRUE.
`noiseEstimation` | Shall noise be estimated (recommended)
`graphical` | Shall the plot of the regressed injection peak be shown.
`...` | Supplementary arguments to be passed to findFIAsignal, see `findFIASignal`.

### Value

A proFIAset object.

### See Also

To obtain more detail about the output see `proFIAset-class`.

### Examples

    if(require("plasFIA")){

    pathplas<-system.file(package="plasFIA","mzML")

    #Parameters are defined.
    ppm<-2

    plasSet<-proFIAset(pathplas,ppm=ppm,parallel=FALSE)
    plasSet

    ###An example using parallelism with a snow cluster using BiocParallel package.
    ## Not run: plasSet<-proFIAset(pathplas,ppm=ppm,parallel=TRUE,BPPARAM=bpparam("SnowParam"))
    }

[Package proFIA version 1.16.3 Index]