jorainer
commented
1 year ago Note that there are already annotation databases for Salmo sarar available in Bioconductor's AnnotationHub:
> library(AnnotationHub)
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
> ah <- AnnotationHub()
snapshotDate(): 2022-10-26
> query(ah, "Salmo salar")
AnnotationHub with 73 records
# snapshotDate(): 2022-10-26
# $dataprovider: Ensembl, FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,E...
# $species: salmo salar, Salmo salar
# $rdataclass: TwoBitFile, GRanges, EnsDb, SQLiteFile, OrgDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH78891"]]'
title
AH78891 | Ensembl 99 EnsDb for Salmo salar
AH79444 | Salmo_salar.ICSASG_v2.99.abinitio.gtf
... ...
AH107261 | LRBaseDb for Salmo salar (Atlantic salmon, v004)
AH107424 | org.Salmo_salar.eg.sqlite Or if you are specifically interested in an EnsDb database:
> query(ah, c("EnsDb", "Salmo salar"))
AnnotationHub with 9 records
# snapshotDate(): 2022-10-26
# $dataprovider: Ensembl
# $species: Salmo salar
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH78891"]]'
title
AH78891 | Ensembl 99 EnsDb for Salmo salar
AH79796 | Ensembl 100 EnsDb for Salmo salar
... ...
AH100766 | Ensembl 106 EnsDb for Salmo salar
AH104987 | Ensembl 107 EnsDb for Salmo salarYou can then get the one e.g. for Ensembl 107 using:
> query(ah, "Salmo salar")
AnnotationHub with 73 records
# snapshotDate(): 2022-10-26
# $dataprovider: Ensembl, FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,E...
# $species: salmo salar, Salmo salar
# $rdataclass: TwoBitFile, GRanges, EnsDb, SQLiteFile, OrgDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH78891"]]'
title
AH78891 | Ensembl 99 EnsDb for Salmo salar
AH79444 | Salmo_salar.ICSASG_v2.99.abinitio.gtf
... ...
AH107261 | LRBaseDb for Salmo salar (Atlantic salmon, v004)
AH107424 | org.Salmo_salar.eg.sqlite
> query(ah, c("EnsDb", "Salmo salar"))
AnnotationHub with 9 records
# snapshotDate(): 2022-10-26
# $dataprovider: Ensembl
# $species: Salmo salar
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH78891"]]'
title
AH78891 | Ensembl 99 EnsDb for Salmo salar
AH79796 | Ensembl 100 EnsDb for Salmo salar
... ...
AH100766 | Ensembl 106 EnsDb for Salmo salar
AH104987 | Ensembl 107 EnsDb for Salmo salar
> edb <- ah[["AH104987"]]
downloading 1 resources
retrieving 1 resource
|======================================================================| 100%
loading from cache
require(“ensembldb”)If you are however looking for the org database you could get the one listed further above.
db <- ah[["AH107424"]]
Could you please let me know if you will possibly create an Ensembl database for Atlantic salmon (Salmo salar) e.g. for human is org.Hs.eg.db? I found this org.Ss.eg.db for pig. Thanks Marwa