countDistribution

Check case distribution in replicates, chromosomes, and strands.
Check case base composition and filter out other case.patterns.
Then, it generates various plots like bar plots and Venn/Euler diagrams.

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

countDistribution function

<dl><dt>case</dt>
<dd>A Coordinate class object or similar structure for genomic data.</dd>
<dt>genome</dt>
<dd>Genome class object or similar structure.</dd>
<dt>case.pattern</dt>
<dd>String patterns to consider in the analysis.</dd>
<dt>output.path</dt>
<dd>Output path for saving the analysis results.</dd></dl>

Arguments

Function performs an analysis of the distribution of genomic cases. — countDistribution

<dl>

<dt>case</dt>
<dd>A Coordinate class object or similar structure for genomic data.</dd>


<dt>genome</dt>
<dd>Genome class object or similar structure.</dd>


<dt>case.pattern</dt>
<dd>String patterns to consider in the analysis.</dd>


<dt>output.path</dt>
<dd>Output path for saving the analysis results.</dd>

</dl>

countDistribution: Function performs an analysis of the distribution of genomic cases.

Description

Usage

Arguments