geneid.map: Function to find the common genes between two datasets or a...
In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

Description Usage Arguments Value Note Author(s) Examples

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.

1	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`.
`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.

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

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)

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List of 4
 $ geneid1: Named chr [1:54] "10212" "4605" "332" "4171" ...
  ..- attr(*, "names")= chr [1:54] "NM_005804" "NM_002466" "NM_001168" "NM_004526" ...
 $ data1  : num [1:150, 1:54] -0.078 0.321 -0.068 -0.282 -0.178 -0.157 -0.017 0.263 -0.07 -0.156 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:150] "NKI_123" "NKI_327" "NKI_291" "NKI_370" ...
  .. ..$ : chr [1:54] "NM_005804" "NM_002466" "NM_001168" "NM_004526" ...
 $ geneid2: Named chr [1:54] "10212" "4605" "332" "4171" ...
  ..- attr(*, "names")= chr [1:54] "201584_s_at" "201710_at" "202094_at" "202107_s_at" ...
 $ data2  : NULL