findPals: Find palindromes in a bed-formatted dataset

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

Description

Deetects whether the target cytosine overlaps with a palindromic sequences or it is located inbetween of the two arms of a palindromic sequence i.e. in the loop formed by the palindrome.

Usage

findPals(bed.data, offset = 10, min.arm = 5, max.loop = 5,
  max.mismatch = 1)

Arguments

bed.data	A data frame containing input bed-formatted data
offset	Number of nucleotides expanded in each direction (default:10, max:200)
min.arm	Minimum length of each arm (default:5)
max.loop	Maximum length of the loop between the two arms of the palindrome
max.mismatch	The maximum number of mismatching letters allowed between the two arms of the palindromes

Value

1/ DNAString subject with the identified palindromes

2/ Number of palindromes falling on/neighboring input data

3/ Number of palindromes per sequence (input to 'meinter' function)

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