de_pair_chisq: Perform pairwise differential detection tests using...

In AllenInstitute/scrattch.hicat: Hierarchical Iterative Clustering Analysis for Transcriptomic data

Perform pairwise differential detection tests using Chi-Squared for a single pair of clusters

Description

Perform pairwise differential detection tests using Chi-Squared for a single pair of clusters

Usage

de_pair_chisq(pair, cl.present, cl.means, cl.size, genes)

Arguments

pair	a numeric vector of length 2 specifying which clusters to compare
cl.present	a data.frame of gene detection proportions (genes x clusters)
cl.means	a data.frame of normalized mean gene expression values (genes x clusters)
cl.size	a named numeric vector of cluster sizes
genes	the genes to use for pairwise comparisons

Value

a data.frame with DE statistics:

• padj P-values adjusted using the Holm (1979) method (p.adjust() default).

• pval P-values reported by the vec_chisq_test() function.

• lfc Log fold change of mean expression values between the pair of clusters.

• meanA Mean expression value for the first cluster in the pair.

• meanB Mean expression value for the second cluster in the pair.

• q1 Proportion of cells expressing each gene for the first cluster in the pair.

• q2 Proportion of cells expressing each gene for the second cluster in the pair.

AllenInstitute/scrattch.hicat documentation built on June 6, 2024, 5:31 a.m.