refGenome (version 1.7.7)

ensemblGenome-class: Class "ensemblGenome"

Description

ensemblGenome represents ensembl genomic annotation data.

Objects from the Class

Objects can be created by calls of the form ensemblGenome(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.

%

Methods

show

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

%

getGtf

signature(object = "refGenome"): Returns content of gtf table.

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setGtf

signature(object = "refGenome"): Writes content of gtf table.

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getAttr

signature(object = "refGenome"): Returns content of attribute table.

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getGeneTable

signature(object = "refGenome"): Returns content of genes table when table exists. Otherwise NULL is returned.

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setAttr

signature(object = "refGenome"): Writes content of attribute table.

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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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extractPaGenes

signature(object="ensemblGenome"): Extracts all annotations on primary assembly. The function returns a data.frame. Used as shortcut to directly extract a table from gtf files.

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extractFeature

signature(object="ensemblGenome"): Extracts annotated positions which are classified as given 'feature' argument. Returns an 'ensemblGenome' object.

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extractByGeneName

signature(object="ensemblGenome", geneNames="character"): Extracts ensemblGenome object which contains table subsets. When none of the geneNames matches, the function returns NULL.

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extractTranscript

signature(object="ensemblGenome", transcripts="character"): Extracts ensemblGenome object which contains table subsets

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getGenePositions

signature(object="ucscGenome", force="logical"): Extracts table with position data for whole genes (smallest exon start position and largest exon end position. A copy of the table will be placed inside the internal environment. Upon subsequent call only a copy of the contained table is returned unless force=TRUE is given. Upon force=TRUE new gene positions are calculated regardless of existing tables.)

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getGeneTable

signature(object="ucscGenome"): Returns data.frame containing gene-specific data.

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tableTranscript.name

signature(object="ensemblGenome"): Extracts table object which contains tabled 'transcript_name' column of gtf table

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tableTranscript.id

signature(object="ensemblGenome"): Extracts table object which contains tabled 'transcript_id' column of gtf table

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writeDB

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

References

http://www.ensembl.org/info/data/ftp/index.html http://mblab.wustl.edu/GTF22.html#fields

Examples

# NOT RUN {
##-------------------------------------##
## Create an instance from scratch
## Real data:
## ftp://ftp.ensembl.org/pub/release-80/gtf/homo_sapiens/Homo_sapiens.GRCh38.80.gtf.gz
##-------------------------------------##
ens <- ensemblGenome()
basedir(ens) <- system.file("extdata",package="refGenome")
ens_gtf <- "hs.ensembl.62.small.gtf"
read.gtf(ens,ens_gtf)
# Load a previously saved genome:
ensfile <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ensfile)

##-------------------------------------##
## Saving and loading
## Save as R-image (fast loading)
##-------------------------------------##
# }
# NOT RUN {
basedir(ens) <- getwd()
saveGenome(ens, "hs.ensembl.62.small.RData", useBasedir=FALSE)
enr <- loadGenome("hs.ensembl.62.small.RData")
# }
# NOT RUN {
## Save as SQLite database
##-------------------------------------##
## Commented out because RSQlite
## seems to produce memory leaks
##-------------------------------------##
# }
# NOT RUN {
writeDB(ens, filename="ens62.db3", useBasedir=FALSE)
edb <- loadGenomeDb(filename="ens62.db3")
# }
# NOT RUN {
##-------------------------------------##
##Extract data for Primary Assembly seqids
##-------------------------------------##
enpa <- extractSeqids(ens,ensPrimAssembly())
# Tables all features in 'gtf' table
tableFeatures(enpa)
# Extract Coding sequences for Primary Assemblys
enpafeat <- extractFeature(enpa, "exon")
# Shortcut. Returns a data.frame
engen <- extractPaGenes(ens)

##-------------------------------------##
## Extract data for indival Genes
##-------------------------------------##
ddx <- extractByGeneName(ens, "DDX11L1")
ddx
tableTranscript.id(ddx)
tableTranscript.name(ddx)
fam <- extractTranscript(ens, "ENST00000417324")
fam
# Extract range limits of entire Genes
gp <- getGenePositions(ens)
gp
# }