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]$|\.[Nn][Cc]$|\.([Mm][Zz])?[Xx][Mm][Ll]$", recursive = TRUE), snames = gsub("\.[^.]*$", "", basename(files)), sclass = gsub("^\.$", "sample", dirname(files)), profmethod = "bin", profparam = list(), ...)
files |
path names of the NetCDF/mzXML 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 readable 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