Get xcmsset object in one step with optimized methods.

Usage

getdata(
  path,
  index = FALSE,
  BPPARAM = BiocParallel::SnowParam(),
  pmethod = "hplcorbitrap",
  minfrac = 0.67,
  ...
)

Arguments

path: the path to your data
index: the index of the files
BPPARAM: used for BiocParallel package
pmethod: parameters used for different instrumentals such as 'hplcorbitrap', 'uplcorbitrap', 'hplcqtof', 'hplchqtof', 'uplcqtof', 'uplchqtof'. The parameters were from the reference
minfrac: minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group, default 0.67
...: arguments for xcmsSet function

Value

a xcmsset object for that path or selected samples

Details

the parameters are extracted from the papers. If you use name other than the name above, you will use the default setting of XCMS. Also I suggest IPO packages or apLCMS packages to get reasonable data for your own instrumental. If you want to summit the results to a paper, remember to include those parameters.

References

Patti, G. J.; Tautenhahn, R.; Siuzdak, G. Nat. Protocols 2012, 7 (3), 508–516.

Examples

if (FALSE) { # \dontrun{
library(faahKO)
cdfpath <- system.file('cdf', package = 'faahKO')
xset <- getdata(cdfpath, pmethod = ' ')
} # }