annotateEnsembl {iSEE} | R Documentation |
Annotation facility for displaying additional information on selected genes, based on the data retrieved from the ENSEMBL database
annotateEnsembl(se, orgdb, keytype, rowdata_col = NULL, ens_species = gsub(" ", "_", species(orgdb)))
se |
An object that is coercible to SingleCellExperiment. |
orgdb |
An OrgDb object, as a basis for the annotation.
Typical values are |
keytype |
The keytype that matches the IDs used in the |
rowdata_col |
A character string specifying which column of |
ens_species |
Character string containing the species name, coded as in the ENSEMBL database and browser.
For example, |
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.
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) }