findComplexFeatures: Complex feature detection

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

Description

Run the sliding window algorithm to find complex features.

Usage

findComplexFeatures(traces, complex_hypothesis, corr_cutoff = 0.95,
  window_size = 15, parallelized = FALSE, n_cores = 1,
  collapse_method = "apex_only", perturb_cutoff = "5%",
  rt_height = 5, smoothing_length = 11)

Arguments

traces	An object of class traces.
complex_hypothesis	data.table containing complex hypotheses. Should have the following columns: complex_id: character strings, a unique id for every complex complex_name: character strings, a unique name for every complex protein_id: character strings, the protein id, e.g. Uniprot id
corr_cutoff	Numeric, the correlation value for chromatograms above which peptides are considered to be coeluting, default=0.95.
window_size	Integer, size of the window in fractions, default=15
parallelized	Logical, if the computation should be done in parallel, default=FALSE.
n_cores	Integer, the number of cores to use for parallel processing (only applies if parallelized is TRUE), default=1.
collapse_method	Character, method for collapsing multiple features into one feature: "apex_only": collapses by apex "apex_network": collapses by apex and connected network cluster Default="apex_only"
perturb_cutoff	Numeric, the quantile to use in estimating the perturbation level, default="5 Intensity values that are zero are replaced with random values that are below the specified quantile of the input values. Alternatively a cutoff value can be specified as an upper limit for perturbation values. This is nescessary for correlation calculation.
rt_height	Numeric, RT cutoff for collapsing features. Defaults to 5.
smoothing_length	Numeric, smoothing length of Savitzky-Golay filter. Defaults to 11.

Value

A data.table containing protein complex features.

Examples

## Load example data
proteinTraces <- exampleProteinTraces
complexHypotheses <- exampleComplexHypotheses

## Perform co-elution signal detection
complexFeatures <- findComplexFeatures(traces=proteinTraces,
                                       complex_hypothesis=complexHypotheses)

## Inspect complex features
summarizeComplexFeatures(complexFeatures)

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