makeGenomicState: Obtain the genomic state per region from annotation

In lcolladotor/derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

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(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.

Author(s)

Andrew Jaffe, Leonardo Collado-Torres

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")
#
## 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)

lcolladotor/derfinder documentation built on May 4, 2024, 5:38 p.m.