getEnsemblRegionFeatures

Function fetches various genomic features for a specified region from the
Ensembl database. It allows specifying the species, chromosome, region range,
and types of features to query.

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

getEnsemblRegionFeatures function

<dl><dt>species</dt>
<dd>Species name or alias (e.g., homo_sapiens, human).</dd>
<dt>chromosome</dt>
<dd>Chromosome name in Ensembl format (without 'chr' prefix).</dd>
<dt>start</dt>
<dd>Start position of the region.</dd>
<dt>end</dt>
<dd>End position of the region.</dd>
<dt>features</dt>
<dd>List of region features to retrieve from Ensembl. Valid
options include "band", "gene", "transcript", "cds", "exon", "repeat",
"simple", "misc", "variation", "somatic_variation",
"structural_variation", "somatic_structural_variation", "constrained",
"regulatory", "motif", "peak", "other_regulatory", "array_probe", "mane".</dd></dl>

Arguments

Get features of a given region. — getEnsemblRegionFeatures

<dl>

<dt>species</dt>
<dd>Species name or alias (e.g., homo_sapiens, human).</dd>


<dt>chromosome</dt>
<dd>Chromosome name in Ensembl format (without 'chr' prefix).</dd>


<dt>start</dt>
<dd>Start position of the region.</dd>


<dt>end</dt>
<dd>End position of the region.</dd>


<dt>features</dt>
<dd>List of region features to retrieve from Ensembl. Valid
options include "band", "gene", "transcript", "cds", "exon", "repeat",
"simple", "misc", "variation", "somatic_variation",
"structural_variation", "somatic_structural_variation", "constrained",
"regulatory", "motif", "peak", "other_regulatory", "array_probe", "mane".</dd>

</dl>

getEnsemblRegionFeatures: Get features of a given region.

Description

Usage

Value

Arguments