bootstrap_cutoff: Bootstrap Cutoff for SLIDE

In SLIDE: Single Cell Linkage by Distance Estimation is SLIDE

Description

Bootstrap Cutoff for SLIDE

Usage

bootstrap_cutoff(uninfected, fraction = 0.1, iter = 20, level = 0.05)

Arguments

uninfected	A dataframe of protein expression levels in an uninfected subset of cells. All columns must be numeric expression levels.
fraction	Fraction of uninfected cells used for the SLIDE bootstrap. This value should reflect the size of the infected cell population relative to the uninfected cell population. Must be between >0 and <=0.2. Default is 0.1.
iter	Iterations of the SLIDE bootstrap. Default is 20.
level	Alpha level to determine cutoff for a significant mean distance ratio. Default is 0.05.

Value

This function bootstraps a cutoff for the mean distance ratio from the uninfected cell population by running the SLIDE procedure on a random subset of uninfected cells a specified number of times (default 20x). Only to be used if our pre-determined value of 1.2 is insufficient. Depending on how large the uninfected dataset is, this function may take many hours to complete.

References

Sen, N., Mukherjee, G., Sen, A., Bendall, S. C., Sung, P., Nolan, G. P., & Arvin, A. M. (2014). Single-Cell Mass Cytometry Analysis of Human Tonsil T Cell Remodeling by Varicella Zoster Virus. Cell Reports, 8(2), 633–645. https://doi.org/10.1016/j.celrep.2014.06.024

Examples

cutoff <- bootstrap_cutoff(uninfected = UN_sig, fraction = (nrow(I_sig)/nrow(UN_sig)), iter=1)
cutoff

SLIDE documentation built on May 1, 2019, 9:02 p.m.