differential_analysis_scExp: Runs differential analysis between cell clusters

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Description

Based on clusters of cell defined previously, runs non-parametric Wilcoxon Rank Sum test to find significantly depleted or enriched features, in 'one_vs_rest' mode or 'pairwise' mode. In pairwise mode, each cluster is compared to all other cluster individually, and then pairwise comparisons between clusters are combined to find overall differential features using combineMarkers function from scran.

Usage

differential_analysis_scExp(
  scExp,
  de_type = "one_vs_rest",
  method = "wilcox",
  qval.th = 0.01,
  cdiff.th = 1,
  block = NULL
)

Arguments

scExp	A SingleCellExperiment object containing consclust with selected number of cluster.
de_type	Type of comparisons. Either 'one_vs_rest', to compare each cluster against all others, or 'pairwise' to make 1 to 1 comparisons. ('one_vs_rest')
method	Wilcoxon or edgerGLM
qval.th	Adjusted p-value threshold. (0.01)
cdiff.th	Fold change threshold. (1)
block	Use batches as blocking factors ?

Details

This functions takes as input a SingleCellExperiment object with consclust, the type of comparison, either 'one_vs_rest' or 'pairwise', the adjusted p-value threshold (qval.th) and the fold-change threshold (cdiff.th). It outputs a SingleCellExperiment object containing a differential list.

Value

Returns a SingleCellExperiment object containing a differential list.

Examples

data("scExp")
scExp_cf = differential_analysis_scExp(scExp)

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.