Retrieves expression values for one or more genes from the expression matrix using their integer probe IDs.
Arguments
- expression
Numeric matrix of gene expression values as returned by
extract.expression()$expression. Rows are probe IDs, columns are sample IDs.- probe.id
Integer vector of one or more probe IDs as returned by
find.probe.by.gene().
Value
A numeric matrix with one row per probe and one column per sample.
Row names are the probe IDs; column names are the sample IDs. When a
single probe ID is supplied the result is still a matrix (not a vector),
ensuring that build.analysis.df() receives a consistent input type.
Details
The returned matrix is the direct input for build.analysis.df().
Using as.matrix() ensures the single-probe case returns a one-row
matrix rather than a named vector, which keeps the pivot_longer
step in build.analysis.df() consistent regardless of how many genes
are queried.
Examples
# \donttest{
geo <- extract.expression(load.geo.soft(accession = "GDS3268", log.transform = TRUE))
#> GDS3268 not found locally, downloading from NCBI GEO...
#> Using locally cached version of GDS3268 found here:
#> /tmp/RtmpxRZSjV/GDS3268.soft.gz
#> Warning: NaNs produced
#> Using locally cached version of GPL1708 found here:
#> /tmp/RtmpxRZSjV/GPL1708.annot.gz
probes <- find.probe.by.gene(geo$gene, c(
"mucin 20, cell surface associated",
"alcohol dehydrogenase 1A (class I), alpha polypeptide"
))
expr <- get.gene.expression(geo$expression, probes)
dim(expr) # probes x samples
#> [1] 4 202
# }