I have to work with ensemble id's and would like to map Gene identifiers to protein identifiers.
So basically without much reading (except of this https://bioconductor.org/packages/release/bioc/vignettes/AnnotationHub/inst/doc/AnnotationHub-HOWTO.html) I am executing the following sequence of commands. Only modification is that instead of orgDB I am querying for ENSEMBL directly - or so I think (reason being that if going with the orgDB example I do only map 60% of ensembl protein ids to ensembl gene IDs).
library(AnnotationHub) ah = AnnotationHub() ens <- query(ah, "ENSEMBL") ens$species grep("Canis",(unique(ens$species)), value = TRUE) ensmbl_CLF<- query(ah, c("ENSEMBL", "Canis lupus familiaris"))
Which seems to work fine till I hit:
clf <- ensmbl_CLF[] downloading 1 resources retrieving 1 resource |==========================================================================================================================================================================| 100% loading from cache require(“ensembldb”) Error: failed to load resource name: AH67922 title: Ensembl 95 EnsDb for Canis lupus familiaris reason: require(“ensembldb”) failed: use BiocManager::install() to install package? In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘ensembldb’
For sure it is pretty clueless what I am doing, so any answer would be helpfull.