findAltSplicing: Find alternative splicing events

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

Description

Idetifies known alternative splicing events co-localized with input data.

Usage

findAltSplicing(bed.data, known.alt.splice = NULL)

Arguments

bed.data	A data frame containing input bed-formatted data
known.alt.splice	(optional) Full local path to the UCSC knownalt table. If the table is not available locally then the script will fetch known alternative splicing events from UCSC (needs Internet connection).

Value

1/ A data frame with the identified alternative splicing event overlaps (hg19)

2/ A summary table with the frequency of each alternative splicing event compared to the reference frequency

3/ A data frame with the number of alternative splicing events per sequence (input to meinter function)

4/ An overlayed bar chart object

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