get_UTR3CDS: Get 3' UTRs and their last CDS regions based on CP sites

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

Get 3' UTRs and their last CDS regions based on CP sites

Description

Get 3' UTRs and their last CDS regions based on CP sites

Usage

get_UTR3CDS(
  sqlite_db,
  chr.utr3,
  outdir = getInPASOutputDirectory(),
  min.length.diff = 200
)

Arguments

sqlite_db	A path to the SQLite database for InPAS, i.e. the output of setup_sqlitedb().
chr.utr3	An object of GenomicRanges::GRanges, specifying UTR3 GRanges for a chromosome. It must be one element of an output of extract_UTR3Anno().
outdir	A character(1) vector, a path with write permission for storing InPAS analysis results. If it doesn't exist, it will be created.
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

An object of GenomicRanges::GRanges containing GRanges for UTRs with alternative CP sites and the corresponding last CDSs.

Author(s)

Jianhong Ou, Haibo Liu

jianhong/InPAS documentation built on Oct. 27, 2023, 2:13 p.m.