findSpliceSites: Find splice sites

In andigoni/MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

Description

Detects potential splice sites in the proximal region of the input genomic coordinates. The function implements the prediction model proposed by Shapiro and Senapathy (Shapiro MB, Senapathy P. Nucleic Acids Research. 1987;15(17):7155-7174.)

Usage

findSpliceSites(bed.data, persim = 0.8, offset = 10)

Arguments

bed.data	A data frame containing input bed-formatted data
persim	Similarity with the splice site consensus (default:0.8, range between [0,1])
offset	Number of nucleotides expanded in each direction (default:10, min:5, max:50)

Value

1/ A detailed table with the location of the detected splice sites in each sequence and the corresponding similarity score

2/ A summary table with the number of splice sites detected in each sequence (input 'meinter' function)

andigoni/MeinteR documentation built on Oct. 1, 2021, 9:33 p.m.