map2symbol: Maps gene identifiers to official gene symbol

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

Maps gene identifiers to official gene symbol

Description

Maps gene identifiers in the gene expression matrix to official gene symbols for ease of data interpretation in scClustViz UI.

Usage

map2symbol(nge, annotationDB, rownameKeytype)

Arguments

nge	The gene expression matrix, i.e. getExpr(yourDataObject).
annotationDB	The AnnotationDb object.
rownameKeytype	The keytype of the gene identifiers. Can be determined automatically using findKeyType.

Details

If rownames are already official gene symbols, returns null. In this case, addCellMarkersToCGS and labelCellTypes will proceed under the assumption that the gene identifiers in the input data are already official gene symbols.

Value

A named character vector, the output of AnnotationDbi::mapIds where values are gene symbols and names are the input gene identifiers.

See Also

findKeyType,mapIds, addCellMarkersToCGS, and labelCellTypes.

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