signatureCoherence: Evaluate signature coherence.

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Evaluate signature coherence.

Description

Evaluates signature coherence by computing signature score (using runMS) and then calculating correlations between signature components (i.e., gene expression) and signature score. Genes for which correlations do not exceed coherence threshold are dropped and remaining genes are used to calculate new coherent signature.

Usage

signatureCoherence(
  object = NULL,
  ms.result = NULL,
  genelist,
  slot = "data",
  assay = DefaultAssay(object),
  coherence.threshold = 0.1,
  show.grid = T,
  coherent.ms = T,
  cor.method = "spearman",
  ...
)

Arguments

object	Seurat object
ms.result	Output from runMS() for provided genelist. If not specified, signatures are computed using runMS.
genelist	Named list of genes used to compute gene signature.
slot	Seurat slot used for gene expression correlations. Default is 'data.'
assay	Seurat assay. Default is DefaultAssay(object).
coherence.threshold	Coherence threshold. Default is 0.1.
show.grid	Logical to show grid on coherence graph.
coherent.ms	Logical to recompute coherent signature following coherence thresholding.
cor.method	correlation metod used to determine signature coherence. Options: spearman, pearson. Default is spearman.
...	additional parameters passed to scMiko::runMS().

Value

list of results

Author(s)

Nicholas Mikolajewicz

See Also

runMS

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.