Correlate chromatograms

For xcms >= 3.15.3 please use MSnbase::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 MSnbase::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 class 'Chromatogram,Chromatogram'
correlate(
  x,
  y,
  use = "pairwise.complete.obs",
  method = c("pearson", "kendall", "spearman"),
  align = c("closest", "approx"),
  ...
)

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

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

Arguments

x

MSnbase::Chromatogram() or MSnbase::MChromatograms() object.

y

MSnbase::Chromatogram() or MSnbase::MChromatograms() object.

use

character(1) passed to the cor function. See cor() for details.

method

character(1) passed to the cor function. See stats::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

Michael Witting, Johannes Rainer

Examples

library(MSnbase)
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)
#> [1] -0.02314823
compareChromatograms(chr2, chr1)
#> [1] 0.2630029

compareChromatograms(chrs, chrs)
#>           [,1]        [,2]      [,3]
#> [1,] 1.0000000 -0.02314823 0.9954772
#> [2,] 0.2630029  1.00000000 0.5341594
#> [3,] 0.9954772  0.53415936 1.0000000