##Description
The SLIDE R package is an implementation of the Single Cell Linkage
using Distance Estimation (SLIDE) algorithm (Sen et al), to be used to
detect infectious reprogramming of cells in high dimentional flow
cytometry data. The package contains one major function,
slide(), which does the following: 1. Tells us which
protein expression levels are significantly up or downregulated in in
infected cells compared to uninfected cells 2. Tests for statistically
significant evidence for cellular reprogramming under the infectious
condition.
slide() requires two dataframes as input, one with
protein expression levels for an infected subset of cells, and another
with that of uninfected cells. The function returns results as a five
item list.
## Basic example using the default cutoff
slide(infected = I_sig, uninfected = UN_sig)
## Using bootstrap to determine cutoff, then running SLIDE
cutoff <- bootstrap_cutoff(uninfected = UN_sig, fraction = (nrow(I_sig)/nrow(UN_sig)), iter = 40)
slide(infected = I_sig, uninfected = UN_sig, cutoff = cutoff)The development of this R package was supported by National Science Foundation grant DMS-1811866.
Sen, N., Mukherjee, G., and Arvin, A.M. (2015). Single cell mass cytometry reveals remodeling of human T cell phenotypes by varicella zoster virus. Methods 90, 85–94.