create_noncoding_impact_score_df

annovar_csv_path

string that was used to indicate when a score is not available
during annotation with ANNOVAR (default = ".")

na.string

Create Non-coding Impact Score Data Frame

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_noncoding_impact_score_df function

<dl><dt>annovar_csv_path</dt>
<dd>path to 'ANNOVAR' csv output file</dd>
<dt>na.string</dt>
<dd>string that was used to indicate when a score is not available
during annotation with ANNOVAR (default = ".")</dd></dl>

Arguments

Create Non-coding Impact Score Data Frame — create_noncoding_impact_score_df

<dl>

<dt>annovar_csv_path</dt>
<dd>path to 'ANNOVAR' csv output file</dd>


<dt>na.string</dt>
<dd>string that was used to indicate when a score is not available
during annotation with ANNOVAR (default = ".")</dd>

</dl>

create_noncoding_impact_score_df: Create Non-coding Impact Score Data Frame

Description

Usage

Value

Arguments