findKeyType: Automatically determines keytype for AnnotationDb lookup

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

Automatically determines keytype for AnnotationDb lookup

Description

Compares rownames of gene expression matrix with keys for all keytypes in an AnnotationDb object, and returns the keytype with the best match.

Usage

findKeyType(nge, annotationDB)

Arguments

nge	The gene expression matrix, i.e. getExpr(yourDataObject).
annotationDB	The AnnotationDb object.

Details

If the rownames for the gene expression matrix are not official gene symbols (determined by less than 80 percent of rownames matching keys in the SYMBOL keytype of the AnnotationDb object), this function compares rownames of gene expression matrix with keys for all keytypes in an AnnotationDb object, and returns the keytype with the best match.

Value

A character value, the keytype of the AnnotationDb object, to be passed to map2symbol.

See Also

map2symbol

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.