make.cna.densities.plots: Make density plots for normalized counts

In uclahs-cds/public-R-NanoStringNormCNV: Helper Functions to Normalize NanoString CNV Data

Make density plots for normalized counts

Description

Make density plots of copy number calls per sample and per gene

Usage

make.cna.densities.plots(nano.cnas, fname.stem = NULL)

Arguments

nano.cnas	A gene by sample matrix of CNA information (raw ratios or rounded CNA calls)
fname.stem	To use in filename. Description of how CNAs were called is suggested. Defaults to NULL

Details

Make density plots of copy number calls. Done separately for all genes and separately for all samples

Value

None

Author(s)

Cindy Yao and Emilie Lalonde

Examples

## Not run: 
  # load data
  data(NanoString.DNA.norm);
  data(PhenoData);

  # call CNAs
  cnas <- call.cnas.with.pooled.normals(
    normalized.data = NanoString.DNA.norm,
    phenodata = PhenoData
    );
  
	# plot copy number call density for rounded values
	# two plots: per gene and per sample
	make.cna.densities.plots(
		nano.cnas = cnas$rounded
		);

## End(Not run)

uclahs-cds/public-R-NanoStringNormCNV documentation built on May 31, 2024, 9:09 p.m.