parse_TxDb: Extract gene models from a TxDb object

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

Extract gene models from a TxDb object

Description

Extract gene models from a TxDb object and annotate last 3' UTR exons and the last CDSs

Usage

parse_TxDb(
  sqlite_db = NULL,
  TxDb = getInPASTxDb(),
  edb = getInPASEnsDb(),
  genome = getInPASGenome(),
  chr2exclude = getChr2Exclude(),
  outdir = getInPASOutputDirectory()
)

Arguments

sqlite_db	A path to the SQLite database for InPAS, i.e. the output of setup_sqlitedb(). It can be NULL.
TxDb	An object of GenomicFeatures::TxDb
edb	An object of ensembldb::EnsDb
genome	An object of BSgenome::BSgenome
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.
outdir	A character(1) vector, a path with write permission for storing InPAS analysis results. If it doesn't exist, it will be created.

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 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 can be very cumbersome.

Value

A GenomicRanges::GRanges object for gene models

Author(s)

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
seqnames <- seqnames(BSgenome.Hsapiens.UCSC.hg19)
chr2exclude <- c(
  "chrM", "chrMT",
  seqnames[grepl("_(hap\\d+|fix|alt)$",
    seqnames,
    perl = TRUE
  )]
)
parsed_Txdb <- parse_TxDb(sqlite_db, TxDb, edb, genome,
  chr2exclude = chr2exclude
)

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.