refGenome (version 1.7.7)

refGenome-class: Class "refGenome"

Description

refGenome class: Virtual base class for ucscGenome and ensemblGenome.

Objects from the Class

Objects can be created by calls of the form refGenome(dbfile). dbfile represents SQLite database file.

Slots

basedir:

Object of class "character" Directory where SQLite database is written.

%

ev:

Object of class "environment" Environment that contains data structures. Optionally, there are gtf and attr data.frames.

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Methods

show

signature(object = "refGenome"): Creates a sensible printout.

%

tableSeqids

signature(object = "refGenome"): Returns tabled seqids which counts all annotations for each seqid. The regex argument will display, which seqid is covered by regex. Intended as preparation for extractSeqids.

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extractSeqids

signature(object = "refGenome"): Returns a filtered version of object. Only data for the 'regex' specified seqids is contained. The functions 'ucPrimAssembly' and 'ensPrimAssembly' return regular expressions that allow extraction of primary assemblies for UCSC and Ensembl respectively.

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read.gtf

signature(object, filename="transcripts.gtf", sep = "\t", useBasedir=TRUE, comment.char = "#", progress=100000L, ...): Imports content of gtf file. This is the basic mechanism for data import. It works the same way for ucscGenome and for ensemblGenome.

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saveGenome

signature(object = "refGenome", filename="character", useBasedir="logical"): Saves content of all tables to RData file. When useBasedir is set (default), basedir (from basedir-slot) is prefixed.

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writeDB

signature(object = "refGenome"): Copies content of gtf, attr and xref table to database.

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Examples

# NOT RUN {
##-------------------------------------##
## Loading sample data:
##-------------------------------------##
ensfile <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ensfile)
ens
ddx <- extractByGeneName(ens,"DDX11L1")
ddx
ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(ucfile)
uc
ddx <- extractByGeneName(uc,"DDX11L1")
ddx
# }