filterConsecutiveIdStretches: Filter Consecutive Id Stretches in Chromaograms

In CCprofiler/CCprofiler: Complex feature detection using SEC protein chromatograms.

Description

Filter PCP traces based on a minimal length of consecutive ID stretches.

Usage

filterConsecutiveIdStretches(traces, min_stretch_length = 3,
  remove_empty = TRUE)

Arguments

traces	An object of class traces.
min_stretch_length	Numeric integer, the minimal length a stretch of continuous identifications has to have in order not to be removed. Defaults to 3.
remove_empty	Logical, whether the entries with rowSum == 0 after filtering should be removed, defaults to TRUE.

Value

An object of class traces containing the filtered chromatograms.

Examples

 ## Load example data
 tracesRaw <- examplePeptideTraces
 ## Filter stretches with 3 consecutive ids
 tracesFilteredConSec <- filterConsecutiveIdStretches(tracesRaw,
                                                      min_stretch_length = 3,
                                                      remove_empty = TRUE)
 ## Compare the results
 exampleProtein <- tracesRaw$trace_annotation$protein_id[8]
 plot(subset(tracesRaw,
             trace_subset_type = "protein_id",
             trace_subset_ids = exampleProtein),
      legend= FALSE)
 plot(subset(tracesFilteredConSec,
             trace_subset_type = "protein_id",
             trace_subset_ids = exampleProtein),
      legend= FALSE)

CCprofiler/CCprofiler documentation built on May 19, 2021, 7:40 p.m.