DETest: Differential expression testing

In satabdisaha1288/scBT: What the Package Does (One Line, Title Case)

Differential expression testing

Description

The main function to run any of the statistical tests developed as part of this package for the analysis of single-cell sequencing data.

Usage

DETest(
  sce,
  method = "All",
  verbose = TRUE,
  fixed.priors = TRUE,
  return.time = TRUE
)

Arguments

sce	SingleCellExperiment object with a logcounts assay and a "Dose" column in the rowData(sce)
method	the statistical test(s) to run. Options are "BAYES", "LRT.linear", "LRT.multiple", "ANOVA", "KW", "WRS", "CHISQ", or "MAST". Leave empty to run all tests on your dataset.

Details

Various statistical tests were adapted specifically for dose-response single-cell/single-nuclei transcriptomic data. The method enable the following tests:

1. BAYES is our new Bayes implementation.. what happens when it goes to next line?

2. LRT.linear

Value

a list of data.frames containing the statistical output for each individual tests performed.

References

Authors... 2021

Examples

# Running all statistical tests
DEG.testing <- DETest(sim)

satabdisaha1288/scBT documentation built on June 1, 2025, 4:06 p.m.