lesion_data

Genomic lesion dataset including copy number variations, single nucleotide variants, and structural rearrangements affecting 265 newly diagnosed T-cell Acute Lymphoblastic Leukemia (T-ALL) patients, as reported by Liu, Yu, et al. (2017). The original lesion coordinates were based on the GRCh37 (hg19) human genome assembly. We converted these coordinates to GRCh38 (hg38) using the UCSC LiftOver tool (<a href="https://genome.ucsc.edu/cgi-bin/hgLiftOver">https://genome.ucsc.edu/cgi-bin/hgLiftOver</a>) prior to running GRIN2 analyses.

datasets

Improved version of 'GRIN' software that streamlines its use in practice to analyze genomic lesion data, accelerate its computing, and expand its analysis capabilities to answer additional scientific questions including a rigorous evaluation of the association of genomic lesions with RNA expression. Pounds, Stan, et al. (2013) <DOI:10.1093/bioinformatics/btt372>.

Abdelrahman Elsayed

GRIN2

Genomic Random Interval (GRIN)

Xueyuan Cao

Lakshmi Anuhya patibandla

Stanley Pounds

lesion_data function

<div class="section" id="lesion-data">
<h3><code>lesion_data</code></h3>
A data frame with 6,861 rows and 5 columns:<dl>
<dt>ID</dt>
<dd>Patient identifier for the individual affected by the lesion</dd><dt>chrom</dt>
<dd>Chromosome on which the lesion is located</dd><dt>loc.start</dt>
<dd>Lesion start position (in base pairs, hg38)</dd><dt>loc.end</dt>
<dd>Lesion end position (in base pairs, hg38)</dd><dt>lsn.type</dt>
<dd>Type of lesion (e.g., gain, loss, mutation, fusion, etc.)</dd>
</dl></div>

Format

Genomic lesion dataset including copy number variations, single nucleotide variants, and structural rearrangements affecting 265 newly diagnosed T-cell Acute Lymphoblastic Leukemia (T-ALL) patients, as reported by Liu, Yu, et al. (2017). The original lesion coordinates were based on the GRCh37 (hg19) human genome assembly. We converted these coordinates to GRCh38 (hg38) using the UCSC LiftOver tool (<a href='https://genome.ucsc.edu/cgi-bin/hgLiftOver'>https://genome.ucsc.edu/cgi-bin/hgLiftOver</a>) prior to running GRIN2 analyses.

Example T-ALL Lesion Dataset — lesion_data

<div class='section' id='lesion-data'>
<h3><code>lesion_data</code></h3>


A data frame with 6,861 rows and 5 columns:<dl>
<dt>ID</dt>
<dd>Patient identifier for the individual affected by the lesion</dd>

<dt>chrom</dt>
<dd>Chromosome on which the lesion is located</dd>

<dt>loc.start</dt>
<dd>Lesion start position (in base pairs, hg38)</dd>

<dt>loc.end</dt>
<dd>Lesion end position (in base pairs, hg38)</dd>

<dt>lsn.type</dt>
<dd>Type of lesion (e.g., gain, loss, mutation, fusion, etc.)</dd>


</dl>

</div>

lesion_data: Example T-ALL Lesion Dataset

Description

Usage

Arguments

Format

`lesion_data`