buildRangedKmerTable: Count kmers from a sequence in given ranges and build a...

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Count kmers from a sequence in given ranges and build a data.table of k-mer counts.

Description

Count kmers from a sequence in given ranges and build a data.table of k-mer counts.

Usage

buildRangedKmerTable(
  dna.seq,
  starts,
  ends,
  k,
  method = "sliding",
  chopping.method = "auto",
  remove.N = TRUE
)

Arguments

dna.seq	String of sequence.
starts	Start positions.
ends	End positions.
k	Size of kmer.
method	Method options: "sliding" or "chopping". Chopping consumes a lot of memory for extremely long sequence using "substring" method. Using "Biostrings" for k > 12 is memory consuming. Default is "sliding".
chopping.method	Chopping method: "Biostrings" or "substring". Default is "auto".
remove.N	Remove unknown base N? Default is TRUE.

Value

A data.table object with column kmer and N.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.