get_PAscore: Calculate the CP score

In haibol2016/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Calculate the CP score

Description

Calculate the CP score by using PWM of polyadenylation signal with sequence around given position

Usage

get_PAscore(seqname, pos, str, idx, PWM, genome, ups = 50, dws = 50)

Arguments

seqname	a character(n) vector, the chromosome/scaffold' name
pos	genomic positions
str	DNA strand
idx	offset position
PWM	An R object for a position weight matrix (PWM) for a hexamer polyadenylation signal (PAS), such as AAUAAA.
genome	an object of BSgenome::BSgenome
ups	the number of upstream bases for PAS search.
dws	the number of downstream bases for PAS search.

Value

A list containing offset positions after PA score-based filtering

Author(s)

Jianhong Ou

See Also

get_PAscore2()

haibol2016/InPAS documentation built on Feb. 21, 2025, 6:26 p.m.