FAMEoutliers {TargetSearch} | R Documentation

## FAME outlier detection

### Description

A function to detect retention time marker (FAME) outliers.

### Usage

    FAMEoutliers(samples, RImatrix, pdffile = NA, startDay = NA, endDay = NA,
                 threshold = 3, group.threshold = 0.05)

### Arguments

`samples` | A `tsSample` object created by `ImportSamples` function.
`RImatrix` | A retention time matrix of the found retention time markers.
`pdffile` | A character string naming a PDF file where the FAMEs report will be saved.
`startDay` | A numeric vector with the starting days of your day groups.
`endDay` | A numeric vector with the ending days of your day groups.
`threshold` | A standard deviations cutoff to detect outliers.
`group.threshold` | A numeric cutoff to detect day groups based on hierarchical clustering. Must be between `0..1`.

### Details

If no `pdffile` argument is given, the report will be saved on a file called `"TargetSearch-YYYY-MM-DD.FAME-report.pdf"`, where `YYYY-MM-DD` is a date.

If both `startDay` and `endDay` are not given, the function will try to detect day groups using a hierarchical clustering approach by cutting the tree using `group.threshold` as cutoff height.

Retention time markers that deviate more than `threshold` standard deviations from the mean of their day group will be identified as outliers.

### Value

A logical matrix of the same size of `RImatrix`. A `TRUE` value indicates that the retention time marker in that particular sample is an outlier.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`RIcorrect`, `ImportSamples`, `TSExample`

### Examples

    # load pre-calculated example data and objects
    data(TSExample)

    # find the retention marker outliers of the example data and save it in "outlier.pdf"
    outliers <- FAMEoutliers(sampleDescription, RImatrix, pdffile = "outlier.pdf")

    # find the outliers (although they are reported in the output PDF file)
    apply(outliers, 1, which)

[Package TargetSearch version 1.48.0 Index]