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

Source: R/de.genes.R

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

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.