makeOrgPackageFromNCBI for non model species -> eror in file
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cagenet34 ▴ 20
@cagenet34-10910
Last seen 8 months ago
Toulouse, France, INRA

Hello

I'm trying to make my own package for Ovis Aries. I would like to annotate some DEG obtain with DESeq2 or EdgeR package.

But I obtained the following error :

Error in file(description = tmp, open = "r") : cannot open the connection
In addition: Warning message:
In file(description = tmp, open = "r") :
  cannot open file 'C:/Users/cagenet/Documents/AMHAROC/3_Analyses_bioinfo/Analyse_Stat/EdgeR/gene2pubmed.gz': No such file or directory

Any help will be greatly appreciate. Thank in advance

Carine

 

 

> rm(list=ls())
> workDir <- "C:/Users/cagenet/Documents/AMHAROC/3_Analyses_bioinfo/Analyse_Stat/EdgeR"
> setwd(workDir)
> makeOrgPackageFromNCBI(version = "0.1",
+                        author = "Carine GENET <carine.genet@..fr",
+                        maintainer = "Carine GENET <carine.genet@..fr",
+                        outputDir = ".",
+                        tax_id = "9940",
+                        genus = "Ovis",
+                        species = "aries",
+                        rebuildCache = FALSE)
preparing data from NCBI ...
starting download for 6 data files
getting data for gene2pubmed.gz
Error in file(description = tmp, open = "r") : cannot open the connection
In addition: Warning message:
In file(description = tmp, open = "r") :
  cannot open file 'C:/Users/cagenet/Documents/AMHAROC/3_Analyses_bioinfo/Analyse_Stat/EdgeR/gene2pubmed.gz': No such file or directory
> sessionInfo()
R version 3.3.1 RC (2016-06-17 r70798)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C                   LC_TIME=French_France.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] AnnotationHub_2.4.2    edgeR_3.14.0           limma_3.28.14          AnnotationForge_1.14.2
 [5] org.Hs.eg.db_3.3.0     AnnotationDbi_1.34.3   IRanges_2.6.1          S4Vectors_0.10.1      
 [9] Biobase_2.32.0         BiocGenerics_0.18.0    BiocInstaller_1.22.3  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5                   splines_3.3.1                 xtable_1.8-2                 
 [4] lattice_0.20-33               R6_2.1.2                      httr_1.2.1                   
 [7] tools_3.3.1                   grid_3.3.1                    DBI_0.4-1                    
[10] htmltools_0.3.5               digest_0.6.9                  interactiveDisplayBase_1.10.3
[13] shiny_0.13.2                  rsconnect_0.4.3               mime_0.4                     
[16] RSQLite_1.0.0                 XML_3.98-1.4                  locfit_1.5-9.1               
[19] httpuv_1.3.3                 
makeorgpackagefromncbi • 918 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

You might also consider using the already existing OrgDb that you can get from AnnotationHub:

> hub <- AnnotationHub()
snapshotDate(): 2016-06-06
> query(hub, c("ovis aries","orgdb"))
AnnotationHub with 1 record
# snapshotDate(): 2016-06-06
# names(): AH48021
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Ovis aries
# $rdataclass: OrgDb
# $title: org.Ovis_aries.eg.sqlite
# $description: NCBI gene ID based annotations about Ovis_aries
# $taxonomyid: 9940
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/p...
# $sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: NCBI, Gene, Annotation
# retrieve record with 'object[["AH48021"]]'

> org.Oa.eg.db <- hub[["AH48021"]]

> org.Oa.eg.db
OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Ovis aries
| SPECIES: Ovis aries
| CENTRALID: GID
| Taxonomy ID: 9940
| Db type: OrgDb
| Supporting package: AnnotationDbi

Please see: help('select') for usage information
>
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0
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Perfect ! Fine for me. Thank !!!

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0
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2021: The details of the response have changed. Consider the following, after installing AnnotationHub and defining hub = AnnotationHub::AnnotationHub():

> hub
AnnotationHub with 59557 records
# snapshotDate(): 2021-05-18
# $dataprovider: Ensembl, BroadInstitute, UCSC, ftp://ftp.ncbi.nlm.nih.gov/g...
# $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Bos taurus,...
# $rdataclass: GRanges, TwoBitFile, BigWigFile, EnsDb, Rle, OrgDb, ChainFile...
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH5012"]]' 

            title                               
  AH5012  | Chromosome Band                     
  AH5013  | STS Markers                         
  AH5014  | FISH Clones                         
  AH5015  | Recomb Rate                         
  AH5016  | ENCODE Pilot                        
  ...       ...                                 
  AH95564 | org.Talaromyces_atroroseus.eg.sqlite
  AH95565 | CTCF_hg19.RData                     
  AH95566 | CTCF_hg38.RData                     
  AH95567 | CTCF_mm9.RData                      
  AH95568 | CTCF_mm10.RData                     
> query(hub, c("ovis aries", "orgdb"))
AnnotationHub with 1 record
# snapshotDate(): 2021-05-18
# names(): AH94094
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Ovis aries
# $rdataclass: OrgDb
# $rdatadateadded: 2021-05-18
# $title: org.Ovis_aries.eg.sqlite
# $description: NCBI gene ID based annotations about Ovis aries
# $taxonomyid: 9940
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/p...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH94094"]]' 
> org.Oa.eg.db = hub[["AH94094"]]
loading from cache
> keys(org.Oa.eg.db, keytype="CHR")
 [1] "1"  "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "2"  "20" "21" "22"
[16] "23" "24" "25" "26" "3"  "4"  "5"  "6"  "7"  "8"  "9"  "MT" "Un" "X"
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@valerie-obenchain-4275
Last seen 4 months ago
United States

Try rebuildCache = TRUE. When rebuildCache = FALSE it's assumed you've already downloaded the files necessary to build the Org package. 

Valerie

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Ah ok.I understand, Thank you.

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