Description Usage Arguments Value Author(s) See Also Examples
View source: R/makeGenomicState.R
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.
1 | 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
TxDb
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 | ## 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)
|
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