getdata | R Documentation |
Get xcmsset object in one step with optimized methods.
getdata(
path,
index = FALSE,
BPPARAM = BiocParallel::SnowParam(),
pmethod = "hplcorbitrap",
minfrac = 0.67,
...
)
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 |
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.
a xcmsset object for that path or selected samples
Patti, G. J.; Tautenhahn, R.; Siuzdak, G. Nat. Protocols 2012, 7 (3), 508–516.
getdata2
, getmzrt
## Not run:
library(faahKO)
cdfpath <- system.file('cdf', package = 'faahKO')
xset <- getdata(cdfpath, pmethod = ' ')
## End(Not run)
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