checkGeneRep: Check gene representation

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

Check gene representation

Description

Check whether genes are represented as SYMBOL or ENSEMBL. This is accomplished by comparing query to reference, and using a majority vote.

Usage

checkGeneRep(reference.genes, query.genes)

Arguments

reference.genes	Named vector of genes; names are ENSEMBL, entries are SYMBOL.
query.genes	vector of query genes to check representation

Value

Character specifying ensembl or symbol

Author(s)

Nicholas Mikolajewicz

See Also

ens2sym.so

Examples

## Not run: 
gene.rep <-  checkGeneRep(gNames.list, as.vector(rownames(so.query@assays[[current.assay]]@scale.data)))

if (gene.rep == "ensembl"){
  so.query <- ens2sym.so(so = so.query, gNames.list = gNames.list, convert.RNA = TRUE)
  gene.rep <-  checkGeneRep(gNames.list, as.vector(rownames(so.query@assays[[current.assay]]@scale.data)))
}

## End(Not run)

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