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.
fix_bulk(bulk, mk)Expanded bulk matrix with extra rows for missing genes, filled with zeros.
matrix of bulk RNA-Seq
object of class 'cellMarkers'. See cellMarkers().
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.