get_regionCov: Get coverage for 3' UTR and last CDS regions on a single...

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

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 = getInPASOutputDirectory(),
  phmm = FALSE,
  min.length.diff = 200
)

Arguments

chr.utr3	An object of GenomicRanges::GRanges, 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 character(1) vector, a path with write permission for storing InPAS analysis results. If it doesn't exist, it will be created.
phmm	A logical(1) vector, indicating whether data should be prepared for singleSample analysis? By default, FALSE
min.length.diff	An integer(1) vector, specifying minimal length difference between proximal and distal APA sites which should be met to be considered for differential APA analysis. Default is 200 bp.

Value

coverage view in GRanges

Author(s)

Jianhong Ou, Haibo Liu

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