extractKmers

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.

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

extractKmers function

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

Arguments

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

<dl>

<dt>coor</dt>
<dd>Coordinate class object.</dd>


<dt>genome</dt>
<dd>Genome class object.</dd>


<dt>k</dt>
<dd>Length of k-mer.</dd>


<dt>central.pattern</dt>
<dd>Central pattern of the k-mer, if applicable.</dd>


<dt>rm.overlap.region</dt>
<dd>Boolean indicating if overlapping regions should be
removed. Default is TRUE.</dd>


<dt>verbose</dt>
<dd>Boolean indicating if verbose output is enabled.</dd>

</dl>

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

Description

Usage

Value

Arguments