matchSamples2Samples {metaMS} | R Documentation

## Compare pseudospectra across samples (GC-MS)

### Description

Function `matchSamples2Samples` matches pseudospectra across all samples - if a pseudospectrum is present at more or less the same retention time in several samples, it can get the status of “unknown”. Exactly how much difference there may be between the pseudospectra and retention times, and how often it should be present, is determined by the settings. The auxiliary function `match.unannot.patterns` compares two msp objects, representing experimental samples. Both are not meant to be called directly by the user.

### Usage

    matchSamples2Samples(xset.msp.scaled, xset.msp, annotations, settings)
    match.unannot.patterns(msp1, msp2, settings)

### Arguments

`xset.msp.scaled` | Scaled version of all pseudospectra in the experimental patterns - a nested list, with one entry for each sample, and within every entry an element for each pseudospectrum.
`xset.msp` | Unscaled version of the first argument: both arguments are provided for efficiency reasons.
`annotations` | Annotations of all pseudospectra: only patterns without annotations will be considered.
`settings` | Settings determining what a valid “unknown” is. For an example, see the man page of `FEMsettings`, field `matchIrrelevants`.
`msp1, msp2` | lists of pseudospectra

### Value

Function `matchSamples2Samples` returns an updated annotation object such as the one returned by `matchSamples2DB`, but now with an additional `unknowns` element, containing the pseudospectra that are recognized as “unknowns”.

Function `match.unannot.patterns` returns a list of combinations of pseudospectra IDs, retention times (or retention indices) and match factors (only for those combinations that satisfy the criteria on retention time (index) and match factor).

### Author(s)

Ron Wehrens

[Package metaMS version 1.22.0 Index]