Subset an xcmsRaw object by scans

Subset an xcmsRaw object by scans. The returned xcmsRaw object contains values for all scans specified with argument i. Note that the scanrange slot of the returned xcmsRaw will be c(1, length(object@scantime)) and hence not range(i).

Usage

# S4 method for class 'xcmsRaw,logicalOrNumeric,missing,missing'
x[i, j, drop]

Arguments

x

The xcmsRaw object that should be sub-setted.

i

Integer or logical vector specifying the scans/spectra to which x should be sub-setted.

j

Not supported.

drop

Not supported.

Value

The sub-setted xcmsRaw object.

Details

Only subsetting by scan index in increasing order or by a logical vector are supported. If not ordered, argument i is sorted automatically. Indices which are larger than the total number of scans are discarded.

Author

Johannes Rainer

Examples

## Load a test file
file <- system.file('cdf/KO/ko15.CDF', package = "faahKO")
xraw <- xcmsRaw(file, profstep = 0)
## The number of scans/spectra:
length(xraw@scantime)
#> [1] 1278

## Subset the object to scans with a scan time from 3500 to 4000.
xsub <- xraw[xraw@scantime >= 3500 & xraw@scantime <= 4000]
range(xsub@scantime)
#> [1] 3501.383 3999.039
## The number of scans:
length(xsub@scantime)
#> [1] 319
## The number of values of the subset:
length(xsub@env$mz)
#> [1] 130569