visualize.results: visualize results

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

visualize results

Description

Wrapper function that creates a variety of plots, displaying results

Usage

visualize.results(
  raw.data, normalized.data, phenodata = NULL, cna.rounded = NULL,
  cna.raw = NULL, max.cn = 5, replicate.eval = NULL, exclude.covs = FALSE
  )

Arguments

raw.data	A gene by sample data-frame of raw NanoString counts. First three column names must be 'CodeClass', 'Name', and 'Accession', followed by sample IDs
normalized.data	A gene by sample data-frame of normalized NanoString counts. First three column names must be 'CodeClass', 'Name', and 'Accession', followed by sample IDs
phenodata	A data-frame of sample annotation. Must include columns 'SampleID' and 'Type' and/or 'Cartridge'. Recommended to use output of load.phenodata. Defaults to NULL
cna.rounded	A gene by sample data-frame of CNA calls. See 'cna.rounded' in output of call.cnas.with.matched.normals or call.cnas.with.pooled.normals. Defaults to NULL
cna.raw	A gene by sample data-frame of tumour-normal count ratios. See 'cna.raw' in output of call.cnas.with.matched.normals or call.cnas.with.pooled.normals. Defaults to NULL
max.cn	Maximum allowable ratio in 'cna.raw' data. Sets copy numbers of more than 'max.cn' to 'max.cn'. Defaults to 5
replicate.eval	A list of replicate evaluation results. Use output of evaluate.replicates
exclude.covs	Whether to exclude covariate information (provided in 'phenodata') from plots. Defaults to FALSE

Details

Plots are saved as tiff files to working directory

Value

None

Author(s)

Emilie Lalonde and Dorota Sendorek

Examples

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

  # call CNAs
  cnas <- call.cnas.with.pooled.normals(
    normalized.data = NanoString.DNA.norm,
    phenodata = PhenoData
    );

  # evaluate results
  evaluation <- evaluate.replicates(
    phenodata = PhenoData,
    normalized.data = NanoString.DNA.norm,
    cna.rounded = cnas$rounded
    );

  # plot data and results
  visualize.results(
    raw.data = NanoString.DNA.raw,
    normalized.data = NanoString.DNA.norm,
    phenodata = PhenoData,
    cna.rounded = cnas$rounded,
    cna.raw = cnas$raw,
    replicate.eval = evaluation,
    max.cn = 5
    );   

## End(Not run)

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