annotateEntrez {iSEE} | R Documentation

## Annotation via Entrez database

### Description

Annotation facility for displaying additional information on selected genes, based on the data retrieved from the ENTREZ database

### Usage

    annotateEntrez(se, orgdb, keytype, rowdata_col = NULL)

### Arguments

`se` | An object that is coercible to SingleCellExperiment.
`orgdb` | An OrgDb object, as a basis for the annotation. Typical values are `org.Hs.eg.db` for human, `org.Mm.eg.db` for mouse, and so on. The corresponding package has to be available and loaded before calling this function.
`keytype` | The keytype that matches the IDs used in the `se` object. Can be one of `keytypes(org.XX.eg.db)`, typically `"SYMBOL"`, `"ENSEMBL"`, or `"ENTREZID"`.
`rowdata_col` | A character string specifying which column of `rowData(se)` contains the keys. Defaults to NULL, which corresponds to having the ids of the features as row names of the `se` object itself.

### Value

A function to be used as the value of the `annotFun` parameter of `iSEE`. This function itself returns a `HTML` tag object with the content extracted from the call, accepting as parameters the `se` object and the `row_index` corresponding to the feature of interest.

### Examples

    library(scRNAseq)
    sce <- ReprocessedAllenData(assays="tophat_counts")

    library(org.Mm.eg.db)
    myfun <- annotateEntrez(sce, org.Mm.eg.db, keytype="SYMBOL")
    ## Not run:
    # Requires a working internet connection
    myfun(sce, 4242)

    ## End(Not run)

    # to be used when launching the app itself ----

    app <- iSEE(sce, annotFun = myfun)
    if (interactive()) {
      shiny::runApp(app, port = 1234)
    }

[Package iSEE version 1.6.1 Index]