mapKmers

This function maps k-mers within a specified sequence based on provided start
and end coordinates, or based on a fixed length.

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

mapKmers function

<dl><dt>seq</dt>
<dd>A single sequence string in which k-mers are to be mapped.</dd>
<dt>start</dt>
<dd>A vector of start coordinates for mapping k-mers.
If only start positions are provided, exact k-mer extraction is performed.</dd>
<dt>end</dt>
<dd>A vector of end coordinates corresponding to the start positions.
If NULL, all regions are assumed to have the same length.
Used for varied region lengths to perform a sliding window.</dd>
<dt>len</dt>
<dd>An integer specifying the fixed length of regions.
Used when regions have a uniform length greater than k.
End coordinates are assumed NULL in this case.</dd>
<dt>k</dt>
<dd>An integer specifying the length of k-mers to be mapped.</dd>
<dt>rm.trunc.kmer</dt>
<dd>Logical indicating whether to remove truncated k-mers
resulting from out-of-bound regions. Default is TRUE.</dd></dl>

Arguments

Map k-mers of a given sequence and coordinate — mapKmers

<dl>

<dt>seq</dt>
<dd>A single sequence string in which k-mers are to be mapped.</dd>


<dt>start</dt>
<dd>A vector of start coordinates for mapping k-mers.
If only start positions are provided, exact k-mer extraction is performed.</dd>


<dt>end</dt>
<dd>A vector of end coordinates corresponding to the start positions.
If NULL, all regions are assumed to have the same length.
Used for varied region lengths to perform a sliding window.</dd>


<dt>len</dt>
<dd>An integer specifying the fixed length of regions.
Used when regions have a uniform length greater than k.
End coordinates are assumed NULL in this case.</dd>


<dt>k</dt>
<dd>An integer specifying the length of k-mers to be mapped.</dd>


<dt>rm.trunc.kmer</dt>
<dd>Logical indicating whether to remove truncated k-mers
resulting from out-of-bound regions. Default is TRUE.</dd>

</dl>

mapKmers: Map k-mers of a given sequence and coordinate

Description

Usage

Value

Arguments