findShapes: Find putative conformational DNA changes

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

Description

Predicts conformational changes of DNA shapes, such as minor groove width (MGW), roll, propeller twist (ProT) and helix twist (HeIT) in the unmethylated and methylated context using methyl-DNAshape algorithm.

Usage

findShapes(bed.data, offset = 50, shape.plot = FALSE)

Arguments

bed.data	A data frame containing input bed-formatted data
offset	Number of nucleotides expanded in each direction (default:50, max:200)
shape.plot	A logical flag. If TRUE, the function will display a multi-plot with the conformational changes. (default: FALSE)

Value

1/ p-value of the MGW in the unmethylated/methylated CpG context for each sequence

2/ p-value of the HeIT in the unmethylated/methylated CpG context for each sequence

3/ p-value of the ProT in the unmethylated/methylated CpG context for each sequence

4/ p-value of the Roll in the unmethylated/methylated CpG context for each sequence

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