R: Extract subsets of refGenome by gene-name.

getGenePositions {refGenome} | R Documentation

## Extract subsets of refGenome by gene-name.

### Description

The function searches in the given data for unique `gene_id` values. For each item, values like gene_id, seqid and strand are extracted. Optionally (when present) also gene_name and gene_biotype are extracted. The function assignes unique id values which are ordered by gene_id values (not genetic positions). Owing to this, id values equal `as.numeric(gene_id)`.

### Usage

    getGenePositions(object,by,force=FALSE,...)

### Arguments

`object` | ensemblGenome, ucscGenome or ensemblJunctions. Object from which gene positions are extracted.

`by` | Character. Determines criterion by which genes are discerned. Accepted values: "gene_id" and "gene_name". For Ensembl genomes the default is 'gene_id' and for USCC genomes the default is 'gene_name'.

`force` | Logical. When FALSE, gene positions will only be calculated when a position table is not present in local environment. The function then returns a copy.

`...` | Unused.

### Details

The function stores a copy of the result in the internal environment (`genes` table). Upon subsequent calls the values only are re-calculated when force=TRUE is given. Otherwise the function returns a copy of the contained table. Present `genes` tables will be automatically saved and restored by `saveGenome` and `load.X` functions.

### Value

data.frame

### Author(s)

Wolfgang Kaisers

### Examples

    ##-------------------------------------##
    ## A) Ensembl genome:
    ##-------------------------------------##
    ensfile <- system.file("extdata",
                            "hs.ensembl.62.small.RData", package="refGenome")
    ens <- loadGenome(ensfile)
    gp <- getGenePositions(ens)

    ##-------------------------------------##
    ## B) Ensembl junctions:
    ##-------------------------------------##
    junc <- getSpliceTable(ens)
    genes <- getGenePositions(junc)

    ##-------------------------------------##
    # C) Ucsc genome:
    ##-------------------------------------##
    ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
    uc <- loadGenome(ucfile)
    junc <- getSpliceTable(uc)
    gp <- getGenePositions(junc)

[Package refGenome version 1.7.7 Index]