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(seq_len(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 1.28.0 Index]