create_gene_level_scna_df

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

create_gene_level_scna_df function

<dl><dt>scna_df</dt>
<dd>the SCNA segments data frame. Must contain:<dl>
<dt>chr</dt>
<dd>chromosome the segment is located in</dd></dl></dd><dt>start</dt>
<dd>start position of the segment</dd><dt>end</dt>
<dd>end position of the segment</dd><dt>log2ratio</dt>
<dd>log2 ratio of the segment</dd>
</dl>
<dt>gene_overlap_threshold</dt>
<dd>the percentage threshold for the overlap between
a segment and a transcript (default = 25). This means that if only a segment
overlaps a transcript more than this threshold, the transcript is assigned
the segment's SCNA event.</dd>

Arguments

Create Gene-level SCNA Data Frame — create_gene_level_scna_df

<dl>

<dt>scna_df</dt>
<dd>the SCNA segments data frame. Must contain:<dl>
<dt>chr</dt>
<dd>chromosome the segment is located in</dd>

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

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

<dt>log2ratio</dt>
<dd>log2 ratio of the segment</dd>


</dl></dd>


<dt>gene_overlap_threshold</dt>
<dd>the percentage threshold for the overlap between
a segment and a transcript (default = 25). This means that if only a segment
overlaps a transcript more than this threshold, the transcript is assigned
the segment's SCNA event.</dd>

</dl>

create_gene_level_scna_df: Create Gene-level SCNA Data Frame

Description

Usage

Value

Arguments