Make an OrganismDb object from an existing TxDb object.

Description

The makeOrganismDbFromTxDb function allows the user to make a OrganismDb object from an existing TxDb object.

Usage

makeOrganismDbFromTxDb(txdb, keytype=NA, orgdb=NA)

Arguments

.

.

Details

makeOrganismDbFromTxDb is a convenience function that processes a TxDb object and pairs it up with GO.db and an appropriate OrgDb object to make a OrganismDb object. See ?makeOrganismDbFromBiomart and ?makeOrganismDbFromUCSC for a similar function that feeds data from either a BioMart or UCSC.

Value

A OrganismDb object.

Author(s)

M. Carlson and H. Pages

See Also

• makeOrganismDbFromBiomart for convenient ways to make a OrganismDb object from BioMart online resources.

• The OrganismDb class.

Examples

## lets start with a txdb object
transcript_ids <- c(
    "uc009uzf.1",
    "uc009uzg.1",
    "uc009uzh.1",
    "uc009uzi.1",
    "uc009uzj.1"
)
txdbMouse <- makeTxDbFromUCSC(genome="mm9", tablename="knownGene",
                          transcript_ids=transcript_ids)

## Using that, we can call our function to promote it to an OrgDb object:
odb <- makeOrganismDbFromTxDb(txdb=txdbMouse)

columns(odb)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OrganismDbi)
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 objects are masked from 'package:stats':

    IQR, mad, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OrganismDbi/makeOrganismDbFromTxDb.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeOrganismDbFromTxDb
> ### Title: Make an OrganismDb object from an existing TxDb object.
> ### Aliases: makeOrganismDbFromTxDb
> 
> ### ** Examples
> 
> ## lets start with a txdb object
> transcript_ids <- c(
+     "uc009uzf.1",
+     "uc009uzg.1",
+     "uc009uzh.1",
+     "uc009uzi.1",
+     "uc009uzj.1"
+ )
> txdbMouse <- makeTxDbFromUCSC(genome="mm9", tablename="knownGene",
+                           transcript_ids=transcript_ids)
Error in `genome<-`(`*tmp*`, value = "mm9") : 
  Failed to set session genome to 'mm9'
Calls: makeTxDbFromUCSC -> genome<- -> genome<-
Execution halted