geneid.map: Function to find the common genes between two datasets or a...

In bhklab/genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

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

A list with items:

• 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.

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)

bhklab/genefu documentation built on Nov. 30, 2024, 9:03 p.m.