correlate,Chromatogram,Chromatogram-method {xcms} | R Documentation

## Correlate chromatograms

### Description

For `xcms` >= 3.15.3 please use `compareChromatograms()` instead of `correlate`

Correlate intensities of two chromatograms with each other. If the two `Chromatogram` objects have different retention times they are first aligned to match data points in the first to data points in the second chromatogram. See help on `alignRt` in `MSnbase::Chromatogram()` for more details.

If `correlate` is called on a single `MChromatograms()` object a pairwise correlation of each chromatogram with each other is performed and a `matrix` with the correlation coefficients is returned.

Note that the correlation of two chromatograms depends also on their order, e.g. `correlate(chr1, chr2)` might not be identical to `correlate(chr2, chr1)`. The lower and upper triangular part of the correlation matrix might thus be different.

### Usage

    ## S4 method for signature 'Chromatogram,Chromatogram'
    correlate(
      x,
      y,
      use = "pairwise.complete.obs",
      method = c("pearson", "kendall", "spearman"),
      align = c("closest", "approx"),
      ...
    )

    ## S4 method for signature 'MChromatograms,missing'
    correlate(
      x,
      y = NULL,
      use = "pairwise.complete.obs",
      method = c("pearson", "kendall", "spearman"),
      align = c("closest", "approx"),
      ...
    )

    ## S4 method for signature 'MChromatograms,MChromatograms'
    correlate(
      x,
      y = NULL,
      use = "pairwise.complete.obs",
      method = c("pearson", "kendall", "spearman"),
      align = c("closest", "approx"),
      ...
    )

### Arguments

`x` | `Chromatogram()` or `MChromatograms()` object.
`y` | `Chromatogram()` or `MChromatograms()` object.
`use` | `character(1)` passed to the `cor` function. See `cor()` for details.
`method` | `character(1)` passed to the `cor` function. See `cor()` for details.
`align` | `character(1)` defining the alignment method to be used. See help on `alignRt` in `MSnbase::Chromatogram()` for details. The value of this parameter is passed to the `method` parameter of `alignRt`.
`...` | optional parameters passed along to the `alignRt` method such as `tolerance` that, if set to `0` requires the retention times to be identical.

### Value

`numeric(1)` or `matrix` (if called on `MChromatograms` objects) with the correlation coefficient. If a `matrix` is returned, the rows represent the chromatograms in `x` and the columns the chromatograms in `y`.

### Author(s)

Michael Witting, Johannes Rainer

### Examples

    chr1 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
        intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
    chr2 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
        intensity = c(80, 50, 20, 10, 9, 4, 3, 4, 1, 3))
    chr3 <- Chromatogram(rtime = 3:9 + rnorm(7, sd = 0.3),
        intensity = c(53, 80, 130, 15, 5, 3, 2))

    chrs <- MChromatograms(list(chr1, chr2, chr3))

    ## Using `compareChromatograms` instead of `correlate`.
    compareChromatograms(chr1, chr2)
    compareChromatograms(chr2, chr1)

    compareChromatograms(chrs, chrs)

[Package xcms version 3.16.1 Index]