get_regionCov {InPAS}R Documentation

Get coverage for 3' UTR and last CDS regions on a single chromosome

Description

Get coverage for 3' UTR and last CDS regions on a single chromosome

Usage

get_regionCov(chr.utr3, sqlite_db, outdir, BPPARAM = NULL, phmm = FALSE)

Arguments

chr.utr3

one element of an output of extract_UTR3Anno()

sqlite_db

A path to the SQLite database for InPAS, i.e. the output of setup_sqlitedb().

outdir

A path to a folder for storing coverage data of 3' UTRs and last CDSs on a given chromosome/scaffold. If it doesn't exist, it will be created.

BPPARAM

an optional BiocParallel::BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to bplapply. It can be set to NULL or bpparam()

phmm

A logical(1) vector, indicating whether data should be prepared for singleSample analysis? By default, FALSE

Value

coverage view in GRanges

Author(s)

Jianhong Ou, Haibo Liu


[Package InPAS version 2.2.0 Index]