loadGenome

The Genome object is capable of loading chromosome sequence on demand.
UCSC Genomes are included in this kmeRtone package. Their specific
chromosome sequence will be downloaded on demand once.

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

loadGenome function

<dl><dt>genome.name</dt>
<dd>A genome name. UCSC and NCBI genome is included with
kmeRtone. Input their name e.g. hg19 or GRCh37.</dd>
<dt>fasta.style</dt>
<dd>FASTA version: "UCSC" or "NCBI".</dd>
<dt>mask</dt>
<dd>Genome mask: "none", "soft", or "hard". Default is "none".</dd>
<dt>fasta.path</dt>
<dd>Path to a directory of user-provided genome FASTA files or
the destination to save the NCBI/UCSC downloaded reference genome files.</dd>
<dt>ncbi.db</dt>
<dd>NCBI database: "refseq" or "genbank".</dd>
<dt>ncbi.asm</dt>
<dd>NCBI assembly table.</dd>
<dt>use.UCSC.name</dt>
<dd>For NCBI Genome, use UCSC-style chromosome name? Default
is FALSE.</dd>
<dt>load.limit</dt>
<dd>Maximum chromosome sequences loaded. Default is 1.</dd></dl>

Arguments

Build Genome object. — loadGenome

<dl>

<dt>genome.name</dt>
<dd>A genome name. UCSC and NCBI genome is included with
kmeRtone. Input their name e.g. hg19 or GRCh37.</dd>


<dt>fasta.style</dt>
<dd>FASTA version: "UCSC" or "NCBI".</dd>


<dt>mask</dt>
<dd>Genome mask: "none", "soft", or "hard". Default is "none".</dd>


<dt>fasta.path</dt>
<dd>Path to a directory of user-provided genome FASTA files or
the destination to save the NCBI/UCSC downloaded reference genome files.</dd>


<dt>ncbi.db</dt>
<dd>NCBI database: "refseq" or "genbank".</dd>


<dt>ncbi.asm</dt>
<dd>NCBI assembly table.</dd>


<dt>use.UCSC.name</dt>
<dd>For NCBI Genome, use UCSC-style chromosome name? Default
is FALSE.</dd>


<dt>load.limit</dt>
<dd>Maximum chromosome sequences loaded. Default is 1.</dd>

</dl>

loadGenome: Build Genome object.

Description

Usage

Value

Arguments