calculate_pairwise_overlap: Calculate overlap between proteins

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

Description

Calculates the pairwise overlaps in area under an emission spectra between proteins. Areas are calculated by taking into account the specified channels and excitation by given laser wavelength. Pairs are constructed from all combinations of the given proteins and overlap is reported as a fraction of the area of the second protein in a given pair. For example, the overlap of EGFP by EYFP will likely be different from the overlap of EYFP by EGFP. An overlap of NA means that the area of the second protein is 0 for the given channel (and would result in division by 0). An overlap of 0 means that the relative area of overlapping proteins is practically 0.

Usage

calculate_pairwise_overlap(wavelengths, excitations, emissions, proteins,
  lasers, channels, 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.
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').
threshold	Fraction of total spectral area observed in a given channel that is considered to be practically 0.

Value

A data frame with four columns – protein1, protein2, channel and overlap. Overlap represents the fraction of protein1 area occupied by protein2 in a given channel.

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