MCR_table

A data set containing the minimal common regions (MCRs) across all cancer
types studied in Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ.
Functional genomic analysis of chromosomal aberrations in a compendium of
8000 cancer genomes. Genome Res. 2013;23(2):217-27. Coordinates were converted
to hg19 (from hg18) using UCSC Genome Browser's LiftOver tool.

datasets

Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2021. driveR: driveR: a novel method for
prioritizing cancer driver genes using somatic genomics data. BMC
Bioinformatics <doi:10.1186/s12859-021-04203-7>.

Ege Ulgen

driveR

Prioritizing Cancer Driver Genes Using Genomics Data

MCR_table function

A data frame with 165 rows and 5 variables:<dl>
<dt>chr</dt>
<dd>chromosome the MCR is located in</dd><dt>start</dt>
<dd>start position of the MCR</dd><dt>end</dt>
<dd>end position of the MCR</dd><dt>MCR_type</dt>
<dd>the type ("Amp" or "Del") of the MCR peak</dd><dt>SCNA_density</dt>
<dd>SCNA per Mb within the MCR</dd>
</dl>

Format

Table of Pan-Cancer Minimal Common Regions — MCR_table

A data frame with 165 rows and 5 variables:<dl>
<dt>chr</dt>
<dd>chromosome the MCR is located in</dd>

<dt>start</dt>
<dd>start position of the MCR</dd>

<dt>end</dt>
<dd>end position of the MCR</dd>

<dt>MCR_type</dt>
<dd>the type ("Amp" or "Del") of the MCR peak</dd>

<dt>SCNA_density</dt>
<dd>SCNA per Mb within the MCR</dd>


</dl>

MCR_table: Table of Pan-Cancer Minimal Common Regions

Description

Usage

Arguments

Format