cdsw: Generate Dynamic SWATH Window
In specL: specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Description Usage Arguments Details Value Author(s) See Also Examples

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.

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

`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.

The function determines the SWATH windows using the quantile function.

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.

Christian Panse, Christian Trachsel, 2015, 2016

The S3 class definition: showClass("psmSet")

  # 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)