alterationSummary


<code>facopyInfo</code> object with a certain study's <code>facopy</code> data.



Optional. A character specifying the name of the file to which to output the alteration summary table.


filename


Summary of copy number calls in a <code>facopyInfo</code> object, by alteration type and chromosome arm.


 overview 

facopy is an R package for fine-tuned cancer CNA
association modeling. Association is measured directly at the
genomic features of interest and, in the case of genes,
downstream gene-set enrichment analysis can be performed thanks
to novel internal processing of the data. The software opens a
way to systematically scrutinize the differences in CNA
distribution across tumoral phenotypes, such as those that
relate to tumor type, location and progression. Currently, the
output format from 11 different methods that analyze data from
whole-genome/exome sequencing and SNP microarrays, is
supported. Multiple genomes, alteration types and variable
types are also supported.

David MosenAnsorena

facopy

Feature-based association and gene-set enrichment for copy
number alteration analysis in cancer

alterationSummary function

<code>facopyInfo</code> object with a certain study's <code>facopy</code> data.

Optional. A character specifying the name of the file to which to output the alteration summary table.

Summary of copy number calls in a <code>facopyInfo</code> object, by alteration type and chromosome arm.

alterationSummary: Alteration Summary

Description

Usage

Arguments

Value

Details

Examples