makeGenomicState {derfinder} | R Documentation

## Obtain the genomic state per region from annotation

### Description

This function summarizes the annotation contained in a TxDb at each given base of the genome based on annotated transcripts. It groups contiguous base pairs classified as the same type into regions.

### Usage

    makeGenomicState(txdb, chrs = c(1:22, "X", "Y"), ...)

### Arguments

`txdb` | A TxDb object with chromosome lengths (check `seqlengths(txdb)`). If you are using a TxDb object created from a GFF/GTF file, you will find this https://support.bioconductor.org/p/93235/ useful.
`chrs` | The names of the chromosomes to use as denoted in the `txdb` object. Check isActiveSeq.
`...` | Arguments passed to extendedMapSeqlevels.

### Value

A `GRangesList` object with two elements: `fullGenome` and `codingGenome`. Both have metadata information for the type of region (theRegion), transcript IDs (tx_id), transcript name (tx_name), and gene ID (gene_id). `fullGenome` classifies each region as either being exon, intron or intergenic. `codingGenome` classfies the regions as being promoter, exon, intro, 5UTR, 3UTR or intergenic.

### Author(s)

Andrew Jaffe, Leonardo Collado-Torres

### See Also

TxDb

### Examples

    ## Load the example data base from the GenomicFeatures vignette
    library('GenomicFeatures')
    samplefile <- system.file('extdata', 'hg19_knownGene_sample.sqlite',
        package='GenomicFeatures')
    txdb <- loadDb(samplefile)

    ## Generate genomic state object, only for chr6
    sampleGenomicState <- makeGenomicState(txdb, chrs='chr6')
    ## Not run:
    ## Create the GenomicState object for Hsapiens.UCSC.hg19.knownGene
    txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene

    ## Creating this GenomicState object takes around 8 min for all chrs and
    ## around 30 secs for chr21
    GenomicState.Hsapiens.UCSC.hg19.knownGene.chr21 <-
        makeGenomicState(txdb=txdb, chrs='chr21')

    ## For convinience, this object is already included in derfinder
    library('testthat')
    expect_that(GenomicState.Hsapiens.UCSC.hg19.knownGene.chr21,
       is_equivalent_to(genomicState))

    ## Hsapiens ENSEMBL GRCh37
    library('GenomicFeatures')
    ## Can take several minutes and speed will depend on your internet speed
    xx <- makeTxDbPackageFromBiomart(version = '0.99', maintainer = 'Your Name',
        author='Your Name')
    txdb <- loadDb(file.path('TxDb.Hsapiens.BioMart.ensembl.GRCh37.p11', 'inst',
        'extdata', 'TxDb.Hsapiens.BioMart.ensembl.GRCh37.p11.sqlite'))

    ## Creating this GenomicState object takes around 13 min
    GenomicState.Hsapiens.ensembl.GRCh37.p11 <- makeGenomicState(txdb=txdb,
        chrs=c(1:22, 'X', 'Y'))

    ## Save for later use
    save(GenomicState.Hsapiens.ensembl.GRCh37.p11,
        file='GenomicState.Hsapiens.ensembl.GRCh37.p11.Rdata')

    ## End(Not run)

[Package derfinder version 1.20.0 Index]