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

In FCBF: Fast Correlation Based Filter for Feature Selection

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)

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