Package 'SLIDE'

Bootstrap Cutoff for 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

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Protein Expression Levels in an Infected Cell Sample

Description

Simulated data from an experiment measuring viral reprogramming of lymphocyte surface proteins. These cells demonstrate evidence for significant reprogramming (see vignette for example).

Usage

I_sig

Format

An object of class data.frame with 38 rows and 7 columns.

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Single Cell Linkage by Distance Estimation is SLIDE

Description

Single Cell Linkage by Distance Estimation is SLIDE

Usage

slide(infected, uninfected, cutoff = 1.2)

Arguments

infected	A dataframe of protein expression levels in an infected subset of cells. All columns must be numeric expression levels.
uninfected	A dataframe of protein expression levels in uninfected cells. All columns must be numeric expression levels. This can be interpreted as the population of cells, of which the infected cells are a subset.
cutoff	This is the fold-change in distances being tested from an infected cell to its nearest uninfected and infected cell. The default value is 1.2. Determine an exact value using the bootstrap_cutoff function.

Value

A list with containing five items. Non-parametric testing of up or downregulation in protein expression between the infected and uninfected cells, for both balanced and unbalanced comparisons. Three, it returns a boxplot mirroring these results. Four, the SLIDE Wilcox Rank Sum test results for evidence of cellular remodeling in the infected cells. Fifth, the mean ratio of the distances from each infected cell to its nearest uninfected cell and nearest infected cell.

References

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.

Examples

slide(I_sig, UN_sig)

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Protein Expression Levels in an Uninfected Cell Population

Description

Simulated data from an experiment measuring viral reprogramming of lymphocyte surface proteins. These cells represent the uninfected cell population to which the infected cells will be compared to.

Usage

UN_sig

Format

An object of class data.frame with 781 rows and 7 columns.

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