align-Chromatogram: Aligning chromatographic data

In xcms: LC-MS and GC-MS Data Analysis

Description

Align chromatogram x against chromatogram y. The resulting chromatogram has the same length (number of data points) than y and the same retention times thus allowing to perform any pair-wise comparisons between the chromatograms. If x is a MChromatograms() object, each Chromatogram in it is aligned against y.

Parameter method allows to specify which alignment method should be used. Currently there are the following options:

• method = "matchRtime" (the default): match data points in the first chromatogram (x) to those of the second (y) based on the difference between their retention times: each data point in x is assigned to the data point in y with the smallest difference in their retention times if their difference is smaller than the minimum average difference between retention times in x or y.

• method = "approx": uses the base R approx function to approximate intensities in x to the retention times in y (using linear interpolation). This should only be used for chromatograms that were measured in the same measurement run (e.g. MS1 and corresponding MS2 chromatograms from SWATH experiments).

Usage

## S4 method for signature 'Chromatogram,Chromatogram'
align(x, y, method = c("matchRtime", "approx"), ...)

## S4 method for signature 'MChromatograms,Chromatogram'
align(x, y, method = c("matchRtime", "approx"), ...)

Arguments

x	Chromatogram() or MChromatograms() to be aligned against y.
y	Chromatogram() to which x should be aligned to.
method	character(1)
...	additional parameters to be passed along to the alignment functions.

Value

Chromatogram (or MChromatograms) representing x aligned against y.

Author(s)

Johannes Rainer, Michael Witting

Examples

chr1 <- Chromatogram(rtime = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
    intensity = c(3, 5, 14, 30, 24, 6, 2, 1, 1, 0))
chr2 <- Chromatogram(rtime = c(2.5, 3.42, 4.5, 5.43, 6.5),
    intensity = c(5, 12, 15, 11, 5))

plot(chr1, col = "black")
points(rtime(chr2), intensity(chr2), col = "blue", type = "l")

## Align chr2 to chr1 without interpolation
res <- align(chr2, chr1)
rtime(res)
intensity(res)
points(rtime(res), intensity(res), col = "#00ff0080", type = "l")

## Align chr2 to chr1 with interpolation
res <- align(chr2, chr1, method = "approx")
points(rtime(res), intensity(res), col = "#ff000080", type = "l")

legend("topright", col = c("black", "blue", "#00ff0080", "#ff000080"), lty = 1,
    legend = c("chr1", "chr2", "chr2 matchRtime", "chr2 approx"))

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