geneid.map {genefu} | R Documentation |
This function allows for fast mapping between two datasets or a dataset and a gene list. The mapping process is performed using Entrez Gene id as reference. In case of ambiguities (several probes representing the same gene), the most variant probe is selected.
geneid.map(geneid1, data1, geneid2, data2, verbose = FALSE)
geneid1 |
first vector of Entrez Gene ids. The name of the vector cells must be the name of the probes in the dataset |
data1 |
First dataset with samples in rows and probes in columns. The dimnames must be properly defined. |
geneid2 |
Second vector of Entrez Gene ids. The name of the vector cells must be the name of the probes in the dataset |
data2 |
First dataset with samples in rows and probes in columns. The dimnames must be properly defined. It may be missing. |
verbose |
|
geneid1 |
Mapped gene list from |
data1 |
Mapped dataset from |
geneid2 |
Mapped gene list from |
data2 |
Mapped dataset from |
It is mandatory that the names of geneid1
and geneid2
must be the probe names of the microarray platform.
Benjamin Haibe-Kains
## load NKI data data(nkis) nkis.gid <- annot.nkis[ ,"EntrezGene.ID"] names(nkis.gid) <- dimnames(annot.nkis)[[1]] ## load GGI signature data(sig.ggi) ggi.gid <- sig.ggi[ ,"EntrezGene.ID"] names(ggi.gid) <- as.character(sig.ggi[ ,"probe"]) ## mapping through Entrez Gene ids of NKI and GGI signature res <- geneid.map(geneid1=nkis.gid, data1=data.nkis, geneid2=ggi.gid, verbose=FALSE) str(res)