calPWM

Calculate position weight matrix of overlapping sequences.
Simulation of human population is based on single nucleotide variation.

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

calPWM function

<dl><dt>kmers</dt>
<dd>A vector of k-mers to overlap.</dd>
<dt>pseudo.num</dt>
<dd>Pseudo-number to avoid numerical instability due to lack of
base at a position. Default is zero i.e. no pseudo-number.</dd>
<dt>bg.prop</dt>
<dd>Background proportion of bases. Default is c(a = 0.295,
c = 0.205, g = 0.205, t = 0.295) which is observed in human genome.</dd>
<dt>output</dt>
<dd>Output matrix type. Options are PCM, PPM, and PWM which refer
to position count/probability/weight matrix. Default is PWM.</dd></dl>

Arguments

Calculate position weight matrix of overlapping sequences.
Simulation of human population is based on single nucleotide variation. — calPWM

<dl>

<dt>kmers</dt>
<dd>A vector of k-mers to overlap.</dd>


<dt>pseudo.num</dt>
<dd>Pseudo-number to avoid numerical instability due to lack of
base at a position. Default is zero i.e. no pseudo-number.</dd>


<dt>bg.prop</dt>
<dd>Background proportion of bases. Default is c(a = 0.295,
c = 0.205, g = 0.205, t = 0.295) which is observed in human genome.</dd>


<dt>output</dt>
<dd>Output matrix type. Options are PCM, PPM, and PWM which refer
to position count/probability/weight matrix. Default is PWM.</dd>

</dl>

calPWM: Calculate position weight matrix of overlapping sequences. Simulation of human population is based on single nucleotide variation.

Description

Usage

Value

Arguments