overlappingFeatures: Identify overlapping features

Description Usage Arguments Value Author(s) Examples

View source: R/functions-XCMSnExp.R

Description

overlappingFeatures identifies features that are overlapping or close in the m/z - rt space.

Usage

1

Arguments

x

XCMSnExp with the features.

expandMz

numeric(1) with the value to expand each feature (on each side) in m/z dimension before identifying overlapping features. The resulting "mzmin" for the feature is thus mzmin - expandMz and the "mzmax" mzmax + expandMz.

expandRt

numeric(1) with the value to expand each feature (on each side) in retention time dimension before identifying overlapping features. The resulting "rtmin" for the feature is thus rtmin - expandRt and the "rtmax" rtmax + expandRt.

ppm

numeric(1) to grow the m/z width of the feature by a relative value: mzmin - mzmin * ppm / 2e6, mzmax + mzmax * ppm / 2e6. Each feature is thus expanded in m/z dimension by ppm/2 on each side before identifying overlapping features.

Value

list with indices of features (in featureDefinitions()) that are overlapping.

Author(s)

Johannes Rainer

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
## 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())

## Correspondence analysis
xdata <- groupChromPeaks(faahko_sub, param = PeakDensityParam(sampleGroups = c(1, 1, 1)))

## Identify overlapping features
overlappingFeatures(xdata)

## Identify features that are separated on retention time by less than
## 2 minutes
overlappingFeatures(xdata, expandRt = 60)

xcms documentation built on Nov. 8, 2020, 5:13 p.m.