setAnnotations: set default name of transcription database and name of...
In Mega2R: Accessing and Processing a 'Mega2' Genetic Database
Description
Usage
Arguments
Value
Note
Examples
Description
This function takes two string parameters:
one to specify entrez gene ids to transcripts,
the other to map gene names to entrez gene id's.
Usage
1
setAnnotations(txdb, entrezGene, envir = ENV)
Arguments
txdb
name of Bioconductor transcription database.
entrezGene
name of Bioconductor mapping of gene name or gene alias to entrez gene id
envir
an 'environment' that contains all the data frames created from the SQLite database.
Value
None
Note
Mega2R will take care to load the necessary databases, but you will have to
install them from Bioconductor. This is explained at length in the package Vignette.
Examples
1
2
3
4
5
6
7
db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = read.Mega2DB(db)
setAnnotations("TxDb.Hsapiens.UCSC.hg19.knownGene", "org.Hs.eg.db")
ENV$txdb
ENV$entrezGene
Mega2R documentation built on Dec. 11, 2021, 9:12 a.m.
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Description Usage Arguments Value Note Examples
Description
This function takes two string parameters: one to specify entrez gene ids to transcripts, the other to map gene names to entrez gene id's.
Usage
1 | setAnnotations(txdb, entrezGene, envir = ENV)
|
Arguments
txdb |
name of Bioconductor transcription database. |
entrezGene |
name of Bioconductor mapping of gene name or gene alias to entrez gene id |
envir |
an 'environment' that contains all the data frames created from the SQLite database. |
Value
None
Note
Mega2R will take care to load the necessary databases, but you will have to install them from Bioconductor. This is explained at length in the package Vignette.
Examples
1 2 3 4 5 6 7 | db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = read.Mega2DB(db)
setAnnotations("TxDb.Hsapiens.UCSC.hg19.knownGene", "org.Hs.eg.db")
ENV$txdb
ENV$entrezGene
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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