Calculate gene-wise correlation to target gene profile

Computes the correlation between every gene in a \codeSummarizedExperiment object and a target gene profile across all samples. When multiple target genes are provided, their sample-wise median expression is used as the reference profile.

The target genes can be matched either against row names of the assay matrix or, when available, against \coderowData(se)$gene.

Usage

correlate_genes_to_target(se, gene, assay_name = "conc", method = "spearman")

Arguments

se

A \codeSummarizedExperiment object.

gene

A character vector of one or more target genes.

assay_name

Character. Assay name used for correlation calculation. Default is \code"conc".

method

Character. Correlation method passed to \codestats::cor. Default is \code"pearson".

Value

A data.frame with one row per gene and correlation values. The returned columns include: \describe \itemfeature_idRow names of the assay matrix. \itemgeneGene label. Uses \coderowData(se)$gene when available, otherwise row names. \itemcorrelationCorrelation between each gene and the target profile.