AnnotateDECO {deco} | R Documentation

## DECO annotating function

### Description

This function allows to annotate different ID types using Bioconductor annotation packages (i.e. Homo.sapiens, Mus.musculus, org.Hs.eg.db, org.MeSH.Spo.972h.db, org.Mm.eg.db ...).

### Usage

    AnnotateDECO(ids, id.type, attributes = NA, pack.db = "Homo.sapiens",
                          rm.redundant = TRUE, verbose = FALSE)

### Arguments

`ids` | a character vector including IDs to annotate.
`id.type` | a character indicating what type of ID we are managing. It should match with correct ID types including in annotation package ("Homo.sapiens" by default).
`attributes` | a character indicating which types of ID should annotate the original IDs. It should match with correct ID types including in annotation package (Homo.sapiens by default).
`pack.db` | name of the Bioconductor annotation package to use.
`rm.redundant` | logical indicating if redundant annotation (i.e. two different HGNC symbols for the same EntrezID) should be removed or not.
`verbose` | logical indicating if messages should be displayed.

### Value

This function returns a `data.frame` containing original IDs and corresponding attributes to each one.

### Author(s)

Francisco Jose Campos Laborie <fjcamlab@usal.es>

### Examples

    ##### Annotation example
    # Select an appropiate 'id.type' depending on which annotation
    # package will be used.
    # library(Homo.sapiens)
    # columns(Homo.sapiens)

    # Selecting first 10 original IDs from ALCL dataset
    data(ALCLdata)
    ids <- rownames(assay(ALCL))[1:10]

    ## Not run as example
    # annot <- AnnotateDECO(ids, id.type = "ENSEMBL",
    #                       attributes = c("SYMBOL","CHR","GENENAME"),
    #                       pack.db = "Homo.sapiens", rm.redundant = TRUE)

[Package deco version 1.8.0 Index]