probe2gene | R Documentation |
Transformation of probe level expression to gene level expression
Description
Transforms expression data on probe level to gene level expression by
summarizing all probes that are annotated to a particular gene.
Usage
probe2gene(
probeSE,
chip = NA,
from = "PROBEID",
to = "ENTREZID",
multi.to = "first",
multi.from = "mean"
)
Arguments
probeSE |
Probe expression data. An object of class
SummarizedExperiment . Make sure that the
metadata contains an element named annotation that
provides the corresponding ID of a recognized platform such as
hgu95av2 (Affymetrix Human Genome U95 chip). This requires that a
corresponding .db package exists (see
http://www.bioconductor.org/packages/release/BiocViews.html#___ChipName
for available chips/packages) and that you have it installed.
Alternatively, the mapping from probe to gene can also be defined in the
rowData slot via two columns named (i) PROBEID for the
platform-specific probe ID, and (ii) ENTREZID for the corresponding
NCBI Entrez Gene ID.
|
chip |
Character. The ID of a recognized microarray platform.
Only required if not provided in the metadata of probeSE
via an element named annotation .
|
from |
Character. ID type from which should be mapped. Corresponds to the
ID type of the names of argument se , with the default PROBEID
being appropriate if the mapping is based on Bioconductor annotation packages.
Note that from is ignored if to is a rowData column
of probeSE .
|
to |
Character. Gene ID type to which should be mapped. Corresponds to
the gene ID type the rownames of argument probeSE should be updated with.
Note that this can also be the name of a column in the rowData
slot of probeSE to specify user-defined mappings in which conflicts
have been manually resolved. Defaults to ENTREZID .
|
multi.to |
How to resolve 1:many mappings, i.e. multiple gene IDs for a
single probe ID? This is passed on to the multiVals argument of
mapIds and can thus take several pre-defined values, but also
the form of a user-defined function. However, note that this requires that a
single gene ID is returned for each probe ID. Default is "first" ,
which accordingly returns the first gene ID mapped onto the respective probe ID.
|
multi.from |
How to resolve many:1 mappings, i.e. multiple probe IDs
mapping to the same gene ID? Pre-defined options include:
'mean' (Default): updates the respective gene expression with
the average over the expression of all probes mapping to that gene,
'first': returns the first probe ID for each gene ID with
multiple probe IDs,
'minp' selects the probe ID with minimum p-value (according to the
rowData column PVAL of probeSE ),
'maxfc' selects the probe ID with maximum absolute log2 fold change
(according to the rowData column FC of probeSE ).
|
Value
A SummarizedExperiment
on gene level.
Author(s)
Ludwig Geistlinger
See Also
readSE
for reading expression data from file,
deAna
for differential expression analysis.
Examples
# (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)