derfinder (version 1.6.4)

makeGenomicState: 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.

chrs

The names of the chromosomes to use as denoted in the txdb object. Check isActiveSeq.

...

Arguments passed to other methods and/or advanced arguments.

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

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')
## 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')