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(seq_len(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)