de_pair_limma: Perform pairwise DE tests using limma for a single pair of...

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

Perform pairwise DE tests using limma for a single pair of clusters

Description

Perform pairwise DE tests using limma for a single pair of clusters

Usage

de_pair_limma(pair, cl.present, cl.means, design, fit, 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)
design	a limma design object
fit	a limma fit object
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 limma::eBayes() function.

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

• meanA Normalized mean expression value for the first cluster in the pair.

• meanB Normalized 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 Oct. 20, 2023, 6:55 a.m.