satyanarayan-rao/methyl-dnashaper

R package for high-throughput DNA shape predictions and feature encoding

methyl-DNAshapeR

This packages is an extension of DNAshapeR to profile the fully methylated DNA sequences. User can now use the letter "M" for 5-methylcytosine and the letter "g" for guanine followed by 5-methylcytosine to charecterize methylated site(s).

Using DNAshapeR for methylated sequences

This development version consider two cases for a given sequence. First, it predicts the shape features for unmethylated sequence and second, it methylates specified/all CpG positions and predicts shape features. The prediction also return the difference between shape features (methylated - unmethylated).

Installation guide

Please follow the instructions below to install this package in R environment

library (devtools)
devtools::install_github("satyausc/DNAshapeR") 

Demo

Case I: Methylating all CpG sites in the sequence

library("DNAshapeR")
Pred = getShape ("tmp.fa")
plotShape(Pred$meth.MGW)
plotShape(Pred$unmeth.MGW)
plotShape(Pred$Delta.MGW)

Case II: Methylating specific CpG sites in the sequence

library("DNAshapeR")
Pred = getShape ("tmp.fa", methylated_CpG_pos_file ="pos.fa")
plotShape(Pred$meth.MGW)
plotShape(Pred$unmeth.MGW)
plotShape(Pred$Delta.MGW)