cdsw {specL} | R Documentation

## Generate Dynamic SWATH Window

### Description

This function computes dynamic SWATH windows (`cdsw`) for a given vector of numeric values, an `psmSet` class, or an `specLSet` class. The input R data object can be generated using the `read.bibliospec` function.

### Usage

        cdsw(x, n=20, overlap=1, ...)

### Arguments

`x` | Numeric vector or psmSet class.
`n` | Number of desired SWATH windows. Default is set to 20.
`overlap` | Overlap of SWATH windows. The default is 1 Dalton.
`...` | pass arguments to `hist` function.

### Details

The function determines the SWATH windows using the quantile function.

### Value

The output is `data.frame` having the attributes from, to, mid, width, and counts. In the ideal output all bins should contain the same number of numeric values. This requirement is violated because the window borders are rounded with no digit after the comma.

### Author(s)

Christian Panse, Christian Trachsel, 2015, 2016

### See Also

The S3 class definition: `showClass("psmSet")`

### Examples

      # do not plot histogram
      cdsw(peptideStd, plot = FALSE,  overlap = 0)

      # plot hist
      cdsw(peptideStd, freq = TRUE)

      # pre-filtering
      ## cdsw(x=q1[350 <= q1 & q1 <= 1250], n=20, overlap = 0, freq=TRUE)

[Package specL version 1.28.0 Index]