makeGenomicState {derfinder} | R Documentation |
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(1:22, "X", "Y"), ...)
txdb |
A TxDb object with chromosome lengths
(check |
chrs |
The names of the chromosomes to use as denoted in the
|
... |
Arguments passed to extendedMapSeqlevels. |
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.
Andrew Jaffe, Leonardo Collado-Torres
## 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)