enviGCMS (version 0.7.1)

getdata: Get xcmsset object in one step with optimized methods.

Description

Get xcmsset object in one step with optimized methods.

Usage

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

Value

a xcmsset object for that path or selected samples

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

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.

See Also

getdata2, getmzrt

Examples

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