warning_DA {ChromSCape}R Documentation

Warning for differential_analysis_scExp

Description

Warning for differential_analysis_scExp

Usage

warning_DA(scExp, de_type, method, qval.th, cdiff.th, block, group, ref)

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 ?

group

If de_type is custom, the group to compare (data.frame), must be a one-column data.frame with cell_clusters or sample_id as character in rows

ref

If de_type is custom, the reference to compare (data.frame), must be a one-column data.frame with cell_clusters or sample_id as character in rows

Value

Warnings or Errors if the input are not correct


[Package ChromSCape version 1.4.0 Index]