set_globals: Set up global variables for an InPAS analysis

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

Set up global variables for an InPAS analysis

Description

Set up global variables for an InPAS analysis

Usage

set_globals(
  genome = NULL,
  TxDb = NULL,
  EnsDb = NULL,
  outdir = NULL,
  chr2exclude = c("chrM", "MT", "Pltd", "chrPltd"),
  lockfile = tempfile(tmpdir = getInPASOutputDirectory())
)

Arguments

genome	An object BSgenome::BSgenome. To make things easy, we suggest users creating a BSgenome::BSgenome instance from the reference genome used for read alignment. For details, see the documentation of BSgenome::forgeBSgenomeDataPkg().
TxDb	An object of GenomicFeatures::TxDb
EnsDb	An object of ensembldb::EnsDb
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.
lockfile	A character(1) vector, specifying a file name used for parallel writing to a SQLite database

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