annotateEntrez {iSEE} | R Documentation |
Annotation facility for displaying additional information on selected genes, based on the data retrieved from the ENTREZ database
annotateEntrez(se, orgdb, keytype, rowdata_col = NULL)
se |
An object that is coercible to SingleCellExperiment. |
orgdb |
An OrgDb object, as a basis for the annotation. Typical values can be
|
keytype |
The keytype that matches the IDs used in the |
rowdata_col |
A character string, corresponding to one of the columns (if present) in
|
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,
with parameteres 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) annotateEntrez(sce,org.Mm.eg.db,"SYMBOL") myfun <- annotateEntrez(sce,org.Mm.eg.db,"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 = annotateEntrez(sce,org.Mm.eg.db,"SYMBOL")) if (interactive()) { shiny::runApp(app, port = 1234) }