scDengue: Dengue infected macrophages; gene expression data from GEO...

Description Usage Format Details Source References Examples

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

1

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
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)

FCBF documentation built on Nov. 8, 2020, 8:30 p.m.