[Bioc-devel] Annotation for Lactuca sativa (Lettuce)

[Vincent Carey]

You'll need a current version of R and the AnnotationHub package
installed.  Then

> library(AnnotationHub)

ah *5/39 packages newly attached/loaded, see sessionInfo() for details.*

> ah = AnnotationHub()

*snapshotDate(): 2019-12-26*

> query(ah, "sativa")

AnnotationHub with 7 records

# snapshotDate(): 2019-12-26

# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Inparanoid8

# $species: Oryza sativa_subsp._japonica, Oryza sativa_Japonica_Group,
Oryza...

# $rdataclass: OrgDb, Inparanoid8Db

# additional mcols(): taxonomyid, genome, description,

#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,

#   rdatapath, sourceurl, sourcetype

# retrieve records with, e.g., 'object[["AH10561"]]'


            title

  AH10561 | hom.Oryza_sativa.inp8.sqlite

  AH75771 | org.Camelina_sativa.eg.sqlite

  AH75823 | org.Lactuca_sativa.eg.sqlite

  AH75915 | org.Oryza_sativa_(japonica_cultivar-group).eg.sqlite

  AH75916 | org.Oryza_sativa_Japonica_Group.eg.sqlite

  AH75917 | org.Oryza_sativa_subsp._japonica.eg.sqlite

  AH76047 | org.Cannabis_sativa.eg.sqlite


What then do we have?


> lett = ah[["AH75823"]]

*downloading 1 resources*

*retrieving 1 resource*

*  |======================================================================|
100%*


*loading from cache*

*Loading required package: AnnotationDbi*

*Loading required package: stats4*

*Loading required package: Biobase*

*Welcome to Bioconductor*


*    Vignettes contain introductory material; view with*

*    'browseVignettes()'. To cite Bioconductor, see*

*    'citation("Biobase")', and for packages 'citation("pkgname")'.*



*Attaching package: ‘Biobase’*


*The following object is masked from ‘package:AnnotationHub’:*


*    cache*


*Loading required package: IRanges*

*Loading required package: S4Vectors*


*Attaching package: ‘S4Vectors’*


*The following object is masked from ‘package:base’:*


*    expand.grid*



> lett

OrgDb object:

| DBSCHEMAVERSION: 2.1

| DBSCHEMA: NOSCHEMA_DB

| ORGANISM: Lactuca sativa

| SPECIES: Lactuca sativa

| CENTRALID: GID

| Taxonomy ID: 4236

| Db type: OrgDb

| Supporting package: AnnotationDbi


*Please see: help('select') for usage information*

> keys(lett)[1:10]

 [1] "3772783" "3772784" "3772785" "3772786" "3772787" "3772788" "3772789"

 [8] "3772790" "3772791" "3772792"

> select(lett, keys=.Last.value, columns="GENENAME")

*'select()' returned 1:1 mapping between keys and columns*

       GID                                       GENENAME

1  3772783                                           Ycf2

2  3772784                                           Ycf2

3  3772785                           ribosomal protein S4

4  3772786                      envelope membrane protein

5  3772787                          ribosomal protein S14

6  3772788                      photosystem II protein D1

7  3772789 photosystem I P700 chlorophyll a apoprotein A2

8  3772790                          ribosomal protein S15

9  3772791                       photosystem II protein K

10 3772792                          ribosomal protein L20

> columns(lett)

 [1] "ACCNUM"      "ALIAS"       "CHR"         "ENTREZID"    "EVIDENCE"

 [6] "EVIDENCEALL" "GENENAME"    "GID"         "GO"          "GOALL"

[11] "ONTOLOGY"    "ONTOLOGYALL" "PMID"        "REFSEQ"      "SYMBOL"

[16] "UNIGENE"

>


Please post any followup questions to support.bioconductor.org



On Mon, Jan 6, 2020 at 11:25 AM Camila Alves <alves013 using umn.edu> wrote:

> Hello,
>
> I am looking for Lactuca sativa (lettuce) annotation to download but I am
> not finding it. Do you have it available?
>
> Thank you,
> Camila
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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