get_PAscore {InPAS}R Documentation

calculate the CP score

Description

calculate the CP score by using PWM of polyadenylation signal

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()


[Package InPAS version 2.1.0 Index]