oncoprintPlot: Function to plot genomic events in the style of...

In califano-lab/MOMA: Multi Omic Master Regulator Analysis

Description

Function to plot genomic events in the style of oncoPrint/cBioPortal

Usage

oncoprintPlot(
  summary.vec,
  snpmat.thisClus,
  amps.thisClus,
  dels.thisClus,
  fusions.thisClus,
  important.genes,
  band2gene,
  max.events,
  k
)

Arguments

summary.vec	: named vector of the counts, named 'Event name':'Type' where type is 'mut', 'amp', 'del', 'fus'. Mutations are in Entrez ID Amp/Deletion CNV events are in genomic band location
snpmat.thisClus	: SNP matrix subset to samples in current cluster
amps.thisClus	: CNV matrix subset to samples in current cluster (just amplifications)
dels.thisClus	: CNV matrix subset to samples in current cluster (just deletions)
fusions.thisClus	: Fusion matrix subset to samples in current cluster
important.genes	: well known genes to highlight in the analysis
band2gene	: mapping of genomic location IDs to gene name: vector of HUGO gene ids, named by genomic location
max.events	: maximum number of events to plot for the oncoplots
k	: current cluster number

Value

oncoprint event plot

califano-lab/MOMA documentation built on June 7, 2020, 7:17 a.m.