extractKmers: Extract k-mers from a given Coordinate object and Genome...

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

Extract k-mers from a given Coordinate object and Genome objects

Description

A k-mer table is initialized and updated in every chromosome-loop operation. There are 3 modes of extraction. (1) When k is smaller than 9 or k is larger than 15, the k-mer is extracted in a standard way. A k-mer table with every possible k-mers is created and updated. (2) For k between 9 and 13, the k-mer sequence is split to half to reduce memory usage significantly. e.g. ACGTACGTA will become ACGT ACGTA. (3) When k is larger than 14, k-mers are extracted the same way as (1) but the k-mer table is grown or expanded for every new k-mer found.

Usage

extractKmers(
  coor,
  genome,
  k,
  central.pattern = NULL,
  rm.overlap.region = TRUE,
  verbose = TRUE
)

Arguments

coor	Coordinate class object.
genome	Genome class object.
k	Length of k-mer.
central.pattern	Central pattern of the k-mer, if applicable.
rm.overlap.region	Boolean indicating if overlapping regions should be removed. Default is TRUE.
verbose	Boolean indicating if verbose output is enabled.

Value

A k-mer table with counts for each k-mer.

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