genefu (version 2.4.2)

geneid.map: 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.

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)