R: Class '"ucscGenome"'

ucscGenome-class {refGenome} | R Documentation

## Class `"ucscGenome"`

### Description

ucscGenome class: Represents data stored for UCSC genome. The standard way to import data is to download a "gtf" file from the UCSC Genome Browser (-> Table Browser). Download the "knownGene" Table in output format "GTF". Then import the data via the `read.gtf` function.

### Objects from the Class

Objects can be created by calls of the form `ucscGenome()`.

### 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, attr and additionally xref 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.

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.

writeDB

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

addEnsembl

  `signature(object = "ucscGenome")`: Imports UCSC 'knownToEnsembl' table. It's appended to the gtf table.

addIsoforms

  `signature(object = "ucscGenome")`: Imports UCSC ' knownIsoforms' table. It's appendet to the gtf table.

addXref

  `signature(object = "ucscGenome")`: Imports UCSC 'kgXref' table. A 'geneSymbol' column is added to gtf table. The rest is written into xref table.

extractByGeneName

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

getXref

  `signature(object = "ucscGenome")`: Returns content of xref table.

getGenePositions

  `signature(object="ucscGenome", by="character", 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.

loadGenome

  `signature(filename = "character")`: Imports data from stored R-Environment Image.

loadGenomeDb

  `signature(filename = "character")`: Imports content of object from sqlite3 database.

tableFeatures

  `signature(object="ucscGenome")`: Tables content of "feature" column.

tableTranscript.id

  `signature(object="ucscGenome")`: Tables values in transcript_id column.

extractTranscript

  `signature(object="ucscGenome", transcripts="character")`: Extracts an object which contains data for subset defined by transcript names.

### Author(s)

Wolfgang Kaisers

### References

http://genome.ucsc.edu/

### Examples

    ##-------------------------------------##
    ## Loading and saving
    ## From and to R-image (fast loading)
    ##-------------------------------------##
    ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
    uc <- loadGenome(ucfile)
    uc

    saveGenome(uc, "uc.RData", useBasedir=FALSE)
    ucr <- loadGenome("uc.RData")

    ##-------------------------------------##
    ## Extract data for Primary Assembly seqids
    ##-------------------------------------##
    ucpa <-extractSeqids(uc, ucPrimAssembly())
    # Extract data for indival Genes
    ddx <- extractByGeneName(uc,"DDX11L1")
    ddx
    # Extract range limits of entire Genes
    gp <-getGenePositions(uc)
    gp
    tableFeatures(uc)
    extractByGeneName(ucpa, "DDX11L1")
    tableTranscript.id(ucpa)

    ##-------------------------------------##
    ## Create object from scratch
    ##-------------------------------------##

    uc<-ucscGenome()
    basedir(uc) <- "/my/genome/basedir"
    # Place all UCSC-files in folder
    read.gtf(uc, "knownGene.gtf")
    addXref(uc, "kgXref.csv")
    addEnsembl(uc, "knownToEnsembl.csv")
    addIsoforms(uc, "knownisoforms.csv")

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

[Package refGenome version 1.7.7 Index]