R: Valley detection and centroidization

vdetect {enviPat} | R Documentation

## Valley detection and centroidization

### Description

Checks envelopes calculated by `envelope` for valleys and extracts centroids or intensoids.

### Usage

    vdetect(profiles,detect="centroid",plotit=TRUE,verbose=TRUE)

### Arguments

`profiles` | List of stick profiles as generated by `envelope`.
`detect` | To return either `"centroid"`, `"intensoid"` or `"valley"`.
`plotit` | Should results be plotted, `TRUE/FALSE`?
`verbose` | Verbose, `TRUE/FALSE`?

### Value

List with length equal to length of list `profiles`, with equal names of list entries. Each entry in that list contains the centroids, intensoids or valleys of the envelope in two columns:

`m/z` | m/z
`abundance` | Area (centroid) or abundance (intensoid, valley)

### definitions

Valley: local profile minimum, i.e. any envelope stick flanked by two other sticks of higher abundance.

Stick: see `envelope`.

Centroid mass: intensity-weighted sum of the m/z of sticks between two valleys.

Centroid intensity: profile area between two valleys (mean of upper and lower sum of stick intensities), normalized to the maximum centroid area of the envelope.

Intensoid mass: m/z of the most intense stick between two valleys.

Intensoid intensity: intensity of the most intensive stick between two valleys, normalized to the most intense intensoid.

### Note

Too low stick discretization leads to imprecision in valley, centroid and intensoid characteristics.

### Author(s)

Martin Loos, Christian Gerber

### See Also

`isopattern` `envelope`

### Examples

    ############################
    # batch of chemforms #######
    data(isotopes)
    data(chemforms)
    chemforms<-chemforms[1:5]

    pattern<-isopattern(
      isotopes,
      chemforms,
      threshold=0.1,
      plotit=TRUE,
      charge=FALSE,
      emass=0.00054858,
      algo=2
    )

    profiles<-envelope(
        pattern,
        ppm=FALSE,
        dmz=0.0001,
        frac=1/4,
        env="Gaussian",
        resolution=1E6,
        plotit=TRUE
    )

    centro<-vdetect(
      profiles,
      detect="centroid",
      plotit=TRUE
    )

    ############################

[Package enviPat version 2.4 Index]