map.datasets {genefu} | R Documentation

## Function to map a list of datasets through EntrezGene IDs in order to get the union of the genes

### Description

This function maps a list of datasets through EntrezGene IDs in order to get the union of the genes.

### Usage

    map.datasets(datas, annots, do.mapping = FALSE,
    mapping.coln = "EntrezGene.ID", mapping, verbose = FALSE)

### Arguments

`datas` | List of matrices of gene expressions with samples in rows and probes in columns, dimnames being properly defined.
`annots` | List of matrices of annotations with at least one column named "EntrezGene.ID", dimnames being properly defined.
`do.mapping` | `TRUE` if the mapping through Entrez Gene ids must be performed (in case of ambiguities, the most variant probe is kept for each gene), `FALSE` otherwise.
`mapping.coln` | Name of the column containing the biological annotation to be used to map the different datasets, default is "EntrezGene.ID".
`mapping` | Matrix with columns "EntrezGene.ID" and "probe.x" used to force the mapping such that the probes of platform x are not selected based on their variance.
`verbose` | `TRUE` to print informative messages, `FALSE` otherwise.

### Details

In case of several probes representing the same EntrezGene ID, the most variant is selected if `mapping` is not specified. When a EntrezGene ID does not exist in a specific dataset, NA values are introduced.

### Value

`datas` | List of datasets (gene expression matrices)
`annots` | List of annotations (annotation matrices)

### Author(s)

Benjamin Haibe-Kains

### Examples

    ## load VDX dataset
    data(vdxs)
    ## load NKI dataset
    data(nkis)
    ## reduce datasets
    ginter <- intersect(annot.vdxs[ ,"EntrezGene.ID"], annot.nkis[ ,"EntrezGene.ID"])
    ginter <- ginter[!is.na(ginter)][1:30]
    myx <- unique(c(match(ginter, annot.vdxs[ ,"EntrezGene.ID"]),
      sample(x=1:nrow(annot.vdxs), size=20)))
    data2.vdxs <- data.vdxs[ ,myx]
    annot2.vdxs <- annot.vdxs[myx, ]
    myx <- unique(c(match(ginter, annot.nkis[ ,"EntrezGene.ID"]),
      sample(x=1:nrow(annot.nkis), size=20)))
    data2.nkis <- data.nkis[ ,myx]
    annot2.nkis <- annot.nkis[myx, ]
    ## mapping of datasets
    datas <- list("VDX"=data2.vdxs,"NKI"=data2.nkis)
    annots <- list("VDX"=annot2.vdxs, "NKI"=annot2.nkis)
    datas.mapped <- map.datasets(datas=datas, annots=annots, do.mapping=TRUE)
    str(datas.mapped, max.level=2)

[Package genefu version 2.22.1 Index]