# High-throughput prediction of DNA shape features

## Documentation for package ‘DNAshapeR’ version 1.39.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

DNAshapeR-package | DNAshapeR package for high-throughput prediction of DNA shape features
convertMethFile | Convert fasta file to methylated file format
encodeKmerHbond | encode Hbond
encodeKMerSeq | Encode k-mer DNA sequence features
encodeNstOrderShape | Encode n-st order shape features DNAshapeR can be used to generate feature vectors for a user-defined model. The model can be a shape model. There are four structural parameters including MGW, Roll, ProT and HelT. The second order shape features are product terms of values for the same category of shape features at adjacent positions.
encodeSeqShape | Encode k-mer DNA sequence and n-th order DNA Shape features
getFasta | Extract fasta sequence given a set of genomic intervals and a reference genome.
getShape | Predict DNA shape from a FASTA file
heatShape | Plot heatmap of DNA shape features
normalize | Min-Max normalization
normalizeShape | Normalize n-st order shape features
plotShape | Plot metaprofiles of DNA shape features
readNonStandardFastaFile | Read the position fasta file
readShape | Read (parse) DNA shape predictions
trackShape | Plot track view of DNA shape features