initKmerTable

Initialise k-mer table with the following columns: kmer, pos_strand, and
neg_strand

A multi-purpose and flexible k-meric enrichment analysis software.
'kmeRtone' measures the enrichment of k-mers by comparing the population of
k-mers in the case loci with a carefully devised internal negative control
group, consisting of k-mers from regions close to, yet sufficiently distant
from, the case loci to mitigate any potential sequencing bias. This method
effectively captures both the local sequencing variations and broader
sequence influences, while also correcting for potential biases, thereby
ensuring more accurate analysis. The core functionality of 'kmeRtone' is
the SCORE() function, which calculates the susceptibility scores for k-mers in
case and control regions. Case regions are defined by the genomic coordinates
provided in a file by the user and the control regions can be constructed
relative to the case regions or provided directly. The k-meric susceptibility
scores are calculated by using a one-proportion z-statistic. 'kmeRtone' is
highly flexible by allowing users to also specify their target k-mer patterns
and quantify the corresponding k-mer enrichment scores in the context of
these patterns, allowing for a more comprehensive approach to understanding
the functional implications of specific DNA sequences on a genomic scale
(e.g., CT motifs upon UV radiation damage).
Adib A. Abdullah, Patrick Pflughaupt, Claudia Feng, Aleksandr B. Sahakyan (2024) Bioinformatics (submitted).

Aleksandr B. Sahakyan

kmeRtone

Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Adib Abdullah

Patrick Pflughaupt

Aleksandr Sahakyan

initKmerTable function

<dl><dt>k</dt>
<dd>K-mer size. Limit to 15 because vector size is limited to
.Machine$integer.max. For 9- to 15-mer, the kmer sequence is separated to
two columns (kmer_part1 and kmer_part2) to reduce memory significantly.</dd>
<dt>central.pattern</dt>
<dd>Central pattern(s) of the k-mer. Default is NULL.</dd>
<dt>split.kmer</dt>
<dd>Whether to split the k-mer sequence into two parts for large k values. Default is FALSE.</dd></dl>

Arguments

Initialise k-mer table with all possible k-mers — initKmerTable

<dl>

<dt>k</dt>
<dd>K-mer size. Limit to 15 because vector size is limited to
.Machine$integer.max. For 9- to 15-mer, the kmer sequence is separated to
two columns (kmer_part1 and kmer_part2) to reduce memory significantly.</dd>


<dt>central.pattern</dt>
<dd>Central pattern(s) of the k-mer. Default is NULL.</dd>


<dt>split.kmer</dt>
<dd>Whether to split the k-mer sequence into two parts for large k values. Default is FALSE.</dd>

</dl>

initKmerTable: Initialise k-mer table with all possible k-mers

Description

Usage

Value

Arguments