scDengue {FCBF} | R Documentation

## Dengue infected macrophages; gene expression data from GEO study GSE110496

### Description

Expression data from single cells, from adengue virus infection study by Zanini et al, #' 2018. The expression was filtered to get cells 12 hours after infection with #' a multiplicity of infection (moi) of 1 (dengue) or uninfected(ctrl). Gene counts were normalized via Bioconductor package "SCNorm".

### Usage

    data(scDengue)

### Format

An object of class `SingleCellExperiment`

### Details

Gene expression has to be discretized for use in FCBF.

### Source

GEO

### References

Zanini, F., Pu, S. Y., Bekerman, E., Einav, S., & Quake, S. R. (2018). Single-cell transcriptional dynamics of flavivirus infection. Elife, 7, e32942. PubMed

### Examples

    data(scDengue)
    exprs <- SummarizedExperiment::assay(scDengue, 'logcounts')
    infection <- SummarizedExperiment::colData(scDengue)
    target <- infection$infection
    # Discretize gene expression
    discrete_expression <- as.data.frame(discretize_exprs(exprs))
    fcbf_features <- fcbf(discrete_expression,
                                  target,
                                  thresh = 0.05,
                                  verbose = TRUE)

[Package FCBF version 1.6.0 Index]