build.mismatch.dictionary: Build mismatch dictionary

In ManuSetty/ChIPKernels: String kernels for ChIP-Seq

Description

This build a matrix of distances between all kmers and unique kmers (considering reverse complements).

Usage

  build.mismatch.dictionary(kmer.len, mismatches, out.dir,
    dimismatch = FALSE)

Arguments

kmer.len	Desired length of the kmer
mismatches	Number of mismatches to be allowed
out.dir	Output directory
dimismatch	Boolean indicating if dimismatches should be used. Default is FALSE

Value

Creates a file containing the following elements: pairwise.kmers Distance matrix and kmer.mapping Mapping of reverse complements and kmers to features The filename is constructed based on mismatches, kmer length and kernel used and has the structure: <di>mismatch_dict_kmer<kmer.len_mismatchesmismatches.Rdata

ManuSetty/ChIPKernels documentation built on May 7, 2019, 2:46 p.m.