geneid.map {genefu} | R Documentation

## Function to find the common genes between two datasets or a dataset and a gene list

### Description

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.

### Usage

    geneid.map(geneid1, data1, geneid2, data2, verbose = FALSE)

### Arguments

`geneid1` | first vector of Entrez Gene ids. The name of the vector cells must be the name of the probes in the dataset `data1`.
`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 `data1` if it is not missing, proper names must be assigned otherwise.
`data2` | First dataset with samples in rows and probes in columns. The dimnames must be properly defined. It may be missing.
`verbose` | `TRUE` to print informative messages, `FALSE` otherwise.

### Value

`geneid1` | Mapped gene list from `geneid1`.
`data1` | Mapped dataset from `data1`.
`geneid2` | Mapped gene list from `geneid2`.
`data2` | Mapped dataset from `data2`.

### Note

It is mandatory that the names of `geneid1` and `geneid2` must be the probe names of the microarray platform.

### Author(s)

Benjamin Haibe-Kains

### Examples

    ## 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)

[Package genefu version 2.12.0 Index]