I got error installing the annotation package i made using annotationforge
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shamed • 0
@shamed-22670
Last seen 4.8 years ago

i am doing Gene ontology for my RNAseq data , Salmonella is not a model organisms so that i used annotationforge package to create org.db annotation package for it. then i tried to retieve the package using the below command : install.packages("./org.Senterica.eg.db",repos=NULL) but it gives me error message Warning in install.packages : package ‘./org.Senterica.eg.db’ is not available (for R version 3.6.2)

how can i solve this problem?

annotation • 483 views
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@james-w-macdonald-5106
Last seen 7 hours ago
United States

You don't give near enough information for anybody to help you. In addition, you probably don't need to generate your own OrgDb anyway:

> library(AnnotationHub)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, 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, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
hub <- AnnotationHub()
Bioconductor version 3.10 (BiocManager 1.30.7), ?BiocManager::install for help
> 
  |======================================================================| 100%

snapshotDate(): 2019-10-29
> query(hub, c("salmonella enterica","orgdb"))
AnnotationHub with 4 records
# snapshotDate(): 2019-10-29 
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Salmonella enterica_ser._typhi, Salmonella enterica_serotype_Typ...
# $rdataclass: OrgDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH77103"]]' 

            title                                                          
  AH77103 | org.Salmonella_enterica_ser._typhi.eg.sqlite                   
  AH77104 | org.Salmonella_enterica_serotype_Typhi.eg.sqlite               
  AH77105 | org.Salmonella_enterica_serovar_Typhi.eg.sqlite                
  AH77106 | org.Salmonella_enterica_subsp._enterica_serovar_Typhi.eg.sqlite

So there are four different S. enterica OrgDb databases that you could use without having to generate your own.

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