Resolve Probe IDs to Gene Names

Converts one or more integer probe IDs back to their human-readable gene title strings or short gene symbols using the gene annotation data frame. This is the inverse operation of find.probe.by.gene().

Usage

get.gene.name(genes, probe.id, use.symbols = FALSE)

Arguments

genes

Data frame of gene annotations as returned by extract.expression()$gene. Must contain columns "ID", "Gene title", and "Gene symbol".

probe.id

Integer or character vector of one or more probe IDs to resolve, as returned by find.probe.by.gene().

use.symbols

Logical. If FALSE (default), returns full descriptive gene titles from the "Gene title" column, suitable for interpretation and reporting. If TRUE, returns short gene symbols from the "Gene symbol" column, suitable for plot axis labels and any downstream tool that expects standard gene symbols such as run.gsea().

Value

Character vector of gene names corresponding to the supplied probe IDs. Returns empty strings "" for probes with no annotation, which should be filtered with which(result != "").

Examples

# \donttest{
geo <- extract.expression(load.geo.soft(accession = "GDS507",
                                        log.transform = TRUE))
#> GDS507 not found locally, downloading from NCBI GEO...
#> Using locally cached version of GDS507 found here:
#> /tmp/RtmpxRZSjV/GDS507.soft.gz 
#> Using locally cached version of GPL97 found here:
#> /tmp/RtmpxRZSjV/GPL97.annot.gz 
de.results <- run.limma.de(geo)
#> Removing intercept from test coefficients
top.probes <- rownames(head(de.results, 10))

# Full titles for reporting
top.titles  <- get.gene.name(geo$gene, top.probes)

# Short symbols for plot labels and GSEA
top.symbols <- get.gene.name(geo$gene, top.probes, use.symbols = TRUE)
# }