assess_combinations: Assess protein combinations

In ssokolen/fluoroscripts: Scripts for Importing and Processing Spectrofluorometry Data

Description

Generates all possible combinations of proteins taken n at time, chooses optimal detection channels by selecting those with least overlap and calculates three metrics – max total overlap for the selected channels, sum of all spectral areas for the selected channels, and the ratio of largest calculated area to smallest. Areas are calculated by taking into account excitation by given laser wavelength. As taking n combinations may result in large computation time, it is recommended that some prescreening is performed before running the assessment.

Usage

assess_combinations(wavelengths, excitations, emissions, proteins, n, lasers,
  channels, spectra.threshold = 0.01, channel.threshold = 0.01,
  intensity.threshold = 0.01)

Arguments

wavelengths	A vector of wavelengths (nm).
excitations	A vector of excitation intensities.
emissions	A vector of emmision intensities.
proteins	A vector of protein labels that correspond to each measurement.
n	The number of protein combinations to consider.
lasers	Vector of lasers exciting given proteins e.g. c(488, 642).
channels	Vector of channels for which spectral area is calculated e.g. c('530/30', '670LP').
spectra.threshold	Fraction of total spectral area observed in a given channel that is considered to be practically 0.
channel.threshold	Fraction of maximum area observed within a given channel that is considered to be practically 0 (compared to all channel areas of the protein).
intensity.threshold	Fraction of maximum area observed across all channels that is considered to be practically 0 (compared to selected protein subset).

Value

A data frame listing the combination of protein1, protein2, protein3 individually, combined combination string, maximum overlap, sum of detection areas, ratio of largest area to smallest, and the detection strategy string that combines protein, channel, and channel overlap information.

ssokolen/fluoroscripts documentation built on May 30, 2019, 8:43 a.m.