retrievechrom

This function connects to the UCSC Genome Browser database using the
`rtracklayer` package to retrieve chromosome information. It returns a
`Seqinfo` object, filtering out unwanted chromosomes such as mitochondrial
DNA (`chrM`) and those with alternative contigs (indicated by an underscore
`_`).

The general principle relies on calculating the cumulative signal of nascent
RNA sequencing over the gene body of any given gene or transcription unit.
'tepr' can identify transcription attenuation sites by comparing profile to
a null model which assumes uniform read density over the entirety of the
transcription unit. It can also identify increased or diminished
transcription attenuation by comparing two conditions. Besides rigorous
statistical testing and high sensitivity, a major feature of 'tepr' is its
ability to provide the elongation pattern of each individual gene, including
the position of the main attenuation point when such a phenomenon occurs.
Using 'tepr', users can visualize and refine genome-wide aggregated analyses
of elongation patterns to robustly identify effects specific to subsets of
genes. These metrics are suitable for internal comparisons (between genes in
each condition) and for studying elongation of the same gene in different
conditions or comparing it to a perfect theoretical uniform elongation.

Nicolas Descostes

tepr

Transcription Elongation Profiling

Victor Billon

Gael Cristofari

retrievechrom function

<dl><dt>genomename</dt>
<dd>A character string specifying the UCSC genome name (e.g.,
"hg19" or "mm10").</dd>
<dt>verbose</dt>
<dd>A logical value. If `TRUE`, the function will print messages
during execution, including a list of the chromosomes being kept.</dd>
<dt>filterchrom</dt>
<dd>A logical value. If `TRUE`, mitochondrial and non-canonical
chromosomes are removed. Default is <code>TRUE</code>.</dd></dl>

Arguments

Retrieve chromosome lengths and information for a specified genome. — retrievechrom

<dl>

<dt>genomename</dt>
<dd>A character string specifying the UCSC genome name (e.g.,
"hg19" or "mm10").</dd>


<dt>verbose</dt>
<dd>A logical value. If `TRUE`, the function will print messages
during execution, including a list of the chromosomes being kept.</dd>


<dt>filterchrom</dt>
<dd>A logical value. If `TRUE`, mitochondrial and non-canonical
chromosomes are removed. Default is <code>TRUE</code>.</dd>

</dl>

retrievechrom: Retrieve chromosome lengths and information for a specified genome.

Description

Usage

Value

Arguments

Examples