Obtain the genomic state per region from annotation

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.

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.

See also

TxDb

Author

Andrew Jaffe, Leonardo Collado-Torres

Examples

## Load the example data base from the GenomicFeatures vignette
library("GenomicFeatures")
#> Loading required package: AnnotationDbi
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
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")
#> 'select()' returned 1:1 mapping between keys and columns
#
if (FALSE) {
## 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"
)
}