plotCNAheatmapOverGoI: plots a heatmap of copy numbers, focusing on a gene of...

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

plots a heatmap of copy numbers, focusing on a gene of interest

Description

plots a heatmap of copy numbers, focusing on a gene of interest

Usage

plotCNAheatmapOverGoI(
  gene,
  Rdirectory,
  genome,
  metaDataFile,
  excludeIndividuals = c(),
  excludeSamples = c(),
  GoIakas = c(),
  cpus = 1,
  padding = 3e+06
)

Arguments

Rdirectory	character The Rdirectory where the superFreq run was run.
genome	character. The genome the sample is aligned to. 'hg19', 'hg38' or 'mm10'
padding	numeric. How many basepairs next to the gene to show. default 3e6.
GoI	character vector. Genes of interest.

Details

This function plots a heatmap of copy numbers across the samples, focused at a gene of interest. Can be run after the superFreq run is completed.

ChristofferFlensburg/superFreq documentation built on June 2, 2025, 10:28 a.m.