slide {SLIDE}

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)