proFIAset {proFIA} | R Documentation |
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.
proFIAset( path, ppm, parallel = TRUE, BPPARAM = NULL, noiseEstimation = TRUE, f = c("regression", "TIC"), graphical = FALSE, ... )
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
|
A proFIAset object.
To obtain more detail about the output see proFIAset-class
.
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")) }