refineChromPeaks-filter-intensity: Remove chromatographic peaks based on intensity
In xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Value Author(s) See Also Examples

Remove chromatographic peaks with intensities below the specified threshold. By default, with nValues = 1, all peaks with an intensity >= threshold are retained. Parameter value allows to specify the column of the chromPeaks() matrix that should be used for the filtering (defaults to value = "maxo" and thus evaluating the maximal intensity for each peak). With nValues > 1 it is possible to keep only peaks that have nValues intensities >= threshold. Note that this requires data import from the original MS files and run time of the call can thus be significantly larger. Also, for nValues > 1 parameter value is ignored.

FilterIntensityParam(threshold = 0, nValues = 1L, value = "maxo")

## S4 method for signature 'XCMSnExp,FilterIntensityParam'
refineChromPeaks(
  object,
  param = FilterIntensityParam(),
  msLevel = 1L,
  BPPARAM = bpparam()
)

`threshold`	`numeric(1)` defining the minimal required intensity for a peak to be retained. Defaults to `threshold = 0`.
`nValues`	`integer(1)` defining the number of data points (per chromatographic peak) that have to be `>= threshold`. Defaults to `nValues = 1`.
`value`	`character(1)` specifying the column in `chromPeaks()` that should be used for the comparison. This is ignored for `nValues > 1`.
`object`	XCMSnExp object with identified chromatographic peaks.
`param`	`FilterIntensityParam` object defining the settings for the method.
`msLevel`	`integer(1)` defining the MS level in which peaks should be filtered.
`BPPARAM`	parameter object to set up parallel processing. Uses the default parallel processing setup returned by `bpparam()`. See `bpparam()` for details and examples.

XCMSnExp object with filtererd chromatographic peaks.

Johannes Rainer, Mar Garcia-Aloy

Other chromatographic peak refinement methods: CleanPeaksParam, MergeNeighboringPeaksParam

## Load a test data set with detected peaks
data(faahko_sub)
## Update the path to the files for the local system
dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")

## Disable parallel processing for this example
register(SerialParam())

## Remove all peaks with a maximal intensity below 50000
res <- refineChromPeaks(faahko_sub, param = FilterIntensityParam(threshold = 50000))

nrow(chromPeaks(faahko_sub))
nrow(chromPeaks(res))

all(chromPeaks(res)[, "maxo"] > 50000)

## Keep only chromatographic peaks that have 3 signals above 20000; we
## perform this on the data of a single file.
xdata <- filterFile(faahko_sub)

res <- refineChromPeaks(xdata, FilterIntensityParam(threshold = 20000, nValues = 3))
nrow(chromPeaks(xdata))
nrow(chromPeaks(res))