Description Usage Arguments Value Author(s) See Also Examples
Transforms expression data on probe level to gene level expression by summarizing all probes that are annotated to a particular gene.
1 2 3 4 5 6 7 8 | probe2gene(
probeSE,
chip = NA,
from = "PROBEID",
to = "ENTREZID",
multi.to = "first",
multi.from = "mean"
)
|
probeSE |
Probe expression data. An object of class
|
chip |
Character. The ID of a recognized microarray platform.
Only required if not provided in the |
from |
Character. ID type from which should be mapped. Corresponds to the
ID type of the names of argument |
to |
Character. Gene ID type to which should be mapped. Corresponds to
the gene ID type the rownames of argument |
multi.to |
How to resolve 1:many mappings, i.e. multiple gene IDs for a
single probe ID? This is passed on to the |
multi.from |
How to resolve many:1 mappings, i.e. multiple probe IDs mapping to the same gene ID? Pre-defined options include:
|
A SummarizedExperiment
on gene level.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
readSE
for reading expression data from file,
deAna
for differential expression analysis.
1 2 3 4 5 6 | # (1) reading the expression data from file
exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
cdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser")
rdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser")
probeSE <- readSE(exprs.file, cdat.file, rdat.file)
geneSE <- probe2gene(probeSE)
|
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