fix_bulk: Fix in missing genes in bulk RNA-Seq matrix

In cellGeometry: Geometric Single Cell Deconvolution

Fix in missing genes in bulk RNA-Seq matrix

Description

Fills in missing genes in a bulk RNA-Seq matrix based on the gene signature of a 'cellMarkers' objects. Signature is taken from both the subclass gene set and group gene set.

Usage

fix_bulk(bulk, mk)

Arguments

bulk	matrix of bulk RNA-Seq
mk	object of class 'cellMarkers'. See cellMarkers().

Details

This is a convenience function if you have an existing cellMarkers signature object and you do not want to remove genes from the existing signatures by running updateMarkers() with the desired bulk data, and are prepared to accept the assumption that genes which are missing in the bulk RNA-Seq dataset have zero expression. We recommend you check which signature genes are missing from the bulk data first.

Value

Expanded bulk matrix with extra rows for missing genes, filled with zeros.

cellGeometry documentation built on April 20, 2026, 1:06 a.m.