R: Class '"ensemblGenome"'

ensemblGenome-class {refGenome} | R Documentation

## 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.

setGtf

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

getAttr

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

getGeneTable

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

setAttr

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

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.

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.

extractFeature

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

extractByGeneName

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

extractTranscript

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

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.)

getGeneTable

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

tableTranscript.name

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

tableTranscript.id

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

writeDB

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

### Author(s)

Wolfgang Kaisers

### References

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

### Examples

    ##-------------------------------------##
    ## 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)
    ##-------------------------------------##

    basedir(ens) <- getwd()
    saveGenome(ens, "hs.ensembl.62.small.RData", useBasedir=FALSE)
    enr <- loadGenome("hs.ensembl.62.small.RData")

    ## Save as SQLite database
    ##-------------------------------------##
    ## Commented out because RSQlite
    ## seems to produce memory leaks
    ##-------------------------------------##

    writeDB(ens, filename="ens62.db3", useBasedir=FALSE)
    edb <- loadGenomeDb(filename="ens62.db3")

    ##-------------------------------------##
    ##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

[Package refGenome version 1.7.7 Index]