downloadNCBIGenomes

Supports options for splitting multi-header fasta files and overwriting existing files.

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

downloadNCBIGenomes function

<dl><dt>asm</dt>
<dd>NCBI assembly summary data.table</dd>
<dt>species</dt>
<dd>Species names.</dd>
<dt>db</dt>
<dd>Database record to use: refseq or genbank</dd>
<dt>output.dir</dt>
<dd>Output directory path. Default is current directory.</dd>
<dt>split.fasta</dt>
<dd>NCBI fasta files are multi-header. Split them? Default is
FALSE.</dd>
<dt>overwrite</dt>
<dd>Overwrite any existed genome file? Default is FALSE to skip
the download.</dd></dl>

Arguments

Function downloads genome fasta files from the NCBI FTP database. Users can
provide either organism names or an assembly summary data table. — downloadNCBIGenomes

<dl>

<dt>asm</dt>
<dd>NCBI assembly summary data.table</dd>


<dt>species</dt>
<dd>Species names.</dd>


<dt>db</dt>
<dd>Database record to use: refseq or genbank</dd>


<dt>output.dir</dt>
<dd>Output directory path. Default is current directory.</dd>


<dt>split.fasta</dt>
<dd>NCBI fasta files are multi-header. Split them? Default is
FALSE.</dd>


<dt>overwrite</dt>
<dd>Overwrite any existed genome file? Default is FALSE to skip
the download.</dd>

</dl>

downloadNCBIGenomes: Function downloads genome fasta files from the NCBI FTP database. Users can provide either organism names or an assembly summary data table.

Description

Usage

Value

Arguments