annotateEnsembl {iSEE}R Documentation

Annotation via ENSEMBL database

Description

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

Usage

annotateEnsembl(se, orgdb, keytype, rowdata_col = NULL,
  ens_species = gsub(" ", "_", species(orgdb)))

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 the values of keytypes(org.XX.eg.db), typically being "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.

ens_species

Character string containing the species name, coded as in the ENSEMBL database and browser. For example, "Homo_sapiens" for human and "Mus_musculus". Defaults to species(orgdb), with the whitespace replaced by underscore

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)
data(allen)
sce <- as(allen, "SingleCellExperiment")
library(org.Mm.eg.db)
myfun <- annotateEnsembl(sce, org.Mm.eg.db, keytype="SYMBOL")
myfun(sce, 4242)

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

app <- iSEE(sce, annotFun = myfun)
if (interactive()) {
  shiny::runApp(app, port = 1234)
}
[Package iSEE version 1.2.4 Index]