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flippant

An R package for the automated analysis of dithionite scramblase assays.

Installation

To install the development version, you first need the devtools package.

install.packages("devtools")

Then you can install the flippant package using

library(devtools)
install_bitbucket("jog2030/flippant")

A stable version is available from CRAN and may be installed using

install.packages("flippant")

The manuscript

A manuscript covering the package is in print at BMC Bioinflormatics and its source provided in Rmd form in the inst/manuscript directory. Note that building the manuscript takes around an hour, since it runs the whole analysis, including code benchmarking using an n of 100.

The dataset

The original data is derived from Ploier et al. (2016; Nat Commun 7, 12832) and contained in a zip file in the inst/extdata directory. Each file within the zip archive is a text file. Lines 4 through to the penultimate line contain tab delimited text data.

Functions

scramblase_assay_traces draws time series of relative fluorescence vs. acquisition time, possibly split by experiment.

scramblase_assay_plot draws plots of the probability of at least one flippase vs. the protein to phospholipid ratio.

scramblase_assay_stats calculates the fit constant for each experiment.

scramblase_assay_calculations provides a lower-level overview of model fit details.