proFIAset: Process FIA experiment.

In proFIA: Preprocessing of FIA-HRMS data

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"))
}

proFIA documentation built on March 20, 2021, 6 p.m.