[,xcmsRaw,logicalOrNumeric,missing,missing-method {xcms} | R Documentation

## Subset an xcmsRaw object by scans

### Description

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 signature '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.

### 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.

### Value

The sub-setted `xcmsRaw` object.

### Author(s)

Johannes Rainer

### See Also

`split.xcmsRaw`

### 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)

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

[Package xcms version 3.16.1 Index]