stagewise_DS_DD: Perform two-stage testing on DS and DD analysis results

In HelenaLC/muscat: Multi-sample multi-group scRNA-seq data analysis tools

Perform two-stage testing on DS and DD analysis results

Description

Perform two-stage testing on DS and DD analysis results

Usage

stagewise_DS_DD(res_DS, res_DD, sce = NULL, verbose = FALSE)

Arguments

res_DS	a list of DS testing results as returned by pbDS or mmDS.
res_DD	a list of DD testing results as returned by pbDD (or pbDS with method="DD").
sce	(optional) SingleCellExperiment object containing the data that underlies testing, prior to summarization with aggregateData. Used for validation of inputs in order to prevent unexpected failure/results.
verbose	logical. Should information on progress be reported?

Value

A list of DFrames containing results for each contrast and cluster. Each table contains DS and DD results for genes shared between analyses, as well as results from stagewise testing analysis, namely:

• p_adj: FDR adjusted p-values for the screening hypothesis that a gene is neither DS nor DD (see ?stageR::getAdjustedPValues for details)

• p_val.DS/D: confirmation stage p-values for DS/D

Examples

data(example_sce)

pbs_sum <- aggregateData(example_sce, assay="counts", fun="sum")
pbs_det <- aggregateData(example_sce, assay="counts", fun="num.detected")
  
res_DS <- pbDS(pbs_sum, min_cells=0, filter="none", verbose=FALSE)
res_DD <- pbDD(pbs_det, min_cells=0, filter="none", verbose=FALSE)

res <- stagewise_DS_DD(res_DS, res_DD)
head(res[[1]][[1]]) # results for 1st cluster

HelenaLC/muscat documentation built on Oct. 9, 2024, 11:59 a.m.