Get xcmsset object in one step with optimized methods.
getdata(
path,
index = FALSE,
BPPARAM = BiocParallel::SnowParam(),
pmethod = "hplcorbitrap",
minfrac = 0.67,
...
)
the path to your data
the index of the files
used for BiocParallel package
parameters used for different instrumentals such as 'hplcorbitrap', 'uplcorbitrap', 'hplcqtof', 'hplchqtof', 'uplcqtof', 'uplchqtof'. The parameters were from the reference
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
a xcmsset object for that path or selected samples
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.
Patti, G. J.; Tautenhahn, R.; Siuzdak, G. Nat. Protocols 2012, 7 (3), 508–516.
if (FALSE) {
library(faahKO)
cdfpath <- system.file('cdf', package = 'faahKO')
xset <- getdata(cdfpath, pmethod = ' ')
}