TxDbLite-class: A parent class for lightweight Ensembl and...

In arcolombo/TxDbLite: Lightweight SQLite-based annotation classes/packages for use with arkas

Description

A parent class for lightweight Ensembl and RepBase/RepeatMasker annotations

A parent class for Ensembl based annotations

Repeat Parent Annotation Class

Ercc Based Annotation Class

ArrayControl Based Annotation Class

get transcripts by gene, promoter, tx_biotype, gene_biotype, or biotype_class

Generic for querying genes

get genes by gene_biotype or biotype_class

Usage

## S4 method for signature 'TxDbLite'
dbconn(x)

## S4 method for signature 'TxDbLite'
show(object)

## S4 method for signature 'TxDbLite'
metadata(x, ...)

## S4 method for signature 'TxDbLite'
transcriptsBy(x, by = c("gene", "promoter",
  "tx_biotype", "gene_biotype", "biotype_class"))

genesBy(x, by = c("gene_biotype", "biotype_class"), ...)

## S4 method for signature 'TxDbLite'
genesBy(x, by = c("gene_biotype", "biotype_class"))

Arguments

x	TxDblite SQL-lite database instance
object	TxDbLite SQL-lite annotation database
...	additional parameters releated to annotation database
by	how to split the genes

Value

a GRangesList

a GRangesList

Slots

con

a DBI Connection

tables

a list of annotation entries

arcolombo/TxDbLite documentation built on July 10, 2020, 12:27 a.m.