setAnnotations: set default name of transcription database and name of...

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 Oct. 23, 2020, 8:19 p.m.