extract_UTR3Anno: extract 3' UTR information from a GenomicFeatures::TxDb...

In haibol2016/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

extract 3' UTR information from a GenomicFeatures::TxDb object

Description

extract 3' UTR information from a GenomicFeatures::TxDb object. The 3'UTR is defined as the last 3'UTR fragment for each transcript and it will be cut if there is any overlaps with other exons.

Usage

extract_UTR3Anno(
  sqlite_db,
  TxDb = getInPASTxDb(),
  edb = getInPASEnsDb(),
  genome = getInPASGenome(),
  outdir = getInPASOutputDirectory(),
  chr2exclude = getChr2Exclude(),
  MAX_EXONS_GAP = 10000L
)

Arguments

sqlite_db	A path to the SQLite database for InPAS, i.e. the output of setup_sqlitedb().
TxDb	An object of GenomicFeatures::TxDb
edb	An object of ensembldb::EnsDb
genome	An object of BSgenome::BSgenome
outdir	A character(1) vector, a path with write permission for storing InPAS analysis results. If it doesn't exist, it will be created.
chr2exclude	A character vector, NA or NULL, specifying chromosomes or scaffolds to be excluded for InPAS analysis. chrM and alternative scaffolds representing different haplotypes should be excluded.
MAX_EXONS_GAP	An integer(1) vector, maximal gap sizes between the last known CP sites to a nearest downstream exon. Default is 10 kb for mammalian genomes. For other species, user need to adjust this parameter.

Details

A good practice is to perform read alignment using a reference genome from Ensembl/GenCode including only the primary assembly and build a TxDb and EnsDb using the GTF/GFF files downloaded from the same source as the reference genome, such as BioMart/Ensembl/GenCode. For instruction, see Vignette of the GenomicFeatures. The UCSC reference genomes and their annotation packages can be very cumbersome.

Value

An object of GenomicRanges::GRangesList, containing GRanges for extracted 3' UTRs, and the corresponding last CDSs and next.exon.gap for each chromosome/scaffold. Chromosome

Author(s)

Jianhong Ou, Haibo Liu

Examples

library("EnsDb.Hsapiens.v86")
library("BSgenome.Hsapiens.UCSC.hg19")
library("GenomicFeatures")
## set a sqlite database
bedgraphs <- system.file("extdata", c(
  "Baf3.extract.bedgraph",
  "UM15.extract.bedgraph"
),
package = "InPAS"
)
tags <- c("Baf3", "UM15")
metadata <- data.frame(
  tag = tags,
  condition = c("Baf3", "UM15"),
  bedgraph_file = bedgraphs
)
outdir <- tempdir()

write.table(metadata,
  file = file.path(outdir, "metadata.txt"),
  sep = "\t", quote = FALSE, row.names = FALSE
)
sqlite_db <- setup_sqlitedb(
  metadata =
    file.path(outdir, "metadata.txt"),
  outdir
)

samplefile <- system.file("extdata",
  "hg19_knownGene_sample.sqlite",
  package = "GenomicFeatures"
)
TxDb <- loadDb(samplefile)
edb <- EnsDb.Hsapiens.v86
genome <- BSgenome.Hsapiens.UCSC.hg19
addInPASOutputDirectory(outdir)
seqnames <- seqnames(BSgenome.Hsapiens.UCSC.hg19)
chr2exclude <- c(
  "chrM", "chrMT",
  seqnames[grepl("_(hap\\d+|fix|alt)$",
    seqnames,
    perl = TRUE
  )]
)
utr3 <- extract_UTR3Anno(sqlite_db, TxDb, edb,
  genome = genome,
  chr2exclude = chr2exclude,
  outdir = tempdir(),
  MAX_EXONS_GAP = 10000L
)

haibol2016/InPAS documentation built on Feb. 21, 2025, 6:26 p.m.