xcmsSet {xcms} | R Documentation |
This function handles the construction of xcmsSet objects. It finds peaks in batch mode and pre-sorts files from subdirectories into different classes suitable for grouping.
xcmsSet(files = list.files(pattern = ".[Cc][Dd][Ff]$", recursive = TRUE), snames = gsub(".[^.]*$", "", basename(files)), sclass = gsub("^.$", "sample", dirname(files)), profmethod = "bin", profparam = list(), ...)
files |
path names of the NetCDF files to read |
snames |
sample names |
sclass |
sample classes |
profmethod |
method to use for profile generation |
profparam |
parameters to use for profile generation |
... |
further arguments to the findPeaks method of the
xcmsRaw class
|
The default values of the files
, snames
, and
sclass
arguments cause the function to recursively search
for *.cdf files. The filename without extention is used for the
sample name. The subdirectory path is used for the sample class.
A xcmsSet
object.
Colin A. Smith, csmith@scripps.edu
xcmsSet-class
,
findPeaks
,
profStep
,
profMethod