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Last data update: 2014.03.03

R: Plots for analyzing PureCN solutions

plotAbs

R Documentation

Plots for analyzing PureCN solutions

Description

This function provides various plots for finding correct purity and ploidy combinations in the results of a runAbsoluteCN call.

Usage

plotAbs(res, ids = NULL, type = c("hist", "overview", 
    "BAF", "AF", "LOH", "all"), chr = NULL, germline.only = TRUE, 
    show.contour = FALSE, purity = NULL, ploidy = NULL, 
    ...)

Arguments

`res`	Return object of the runAbsoluteCN() function.
`ids`	Candidate solutions to be plotted. ids=1 will draw the plot for the maximum likelihood solution.
`type`	Different types of plots. "hist" will plot a histogram, assigning log-ratio peaks to integer values. "overview" will plot all local optima, sorted by likelihood. "BAF" plots something like a B-allele frequency plot known from SNP arrays: it plots allele frequencies of germline variants (or most likely germline when status is not available) against copy number. AF plots observed allelic fractions against expected (purity), maximum likelihood (optimal multiplicity) allelic fractions. "all" plots all, and is useful for generate a PDF for a sample for manual inspection.
`chr`	If NULL, show all chromosomes, otherwise only the ones specified (type=BAF only).
`germline.only`	If TRUE, show only variants most likely being germline in BAF plot. Useful to set to FALSE (in combination with chr) to study potential artifacts.
`show.contour`	For type overview, display contour plot.
`purity`	Display expected integer copy numbers for purity, defaults to purity of the solution (type=hist only).
`ploidy`	Display expected integer copy numbers for ploidy, defaults to ploidy of the solution (type=hist only).
`...`	Additonal parameters passed to the plot() function.

Value

Returns NULL

Author(s)

Markus Riester

Examples

data(purecn.example.output)
plotAbs(purecn.example.output, type="overview")
# plot details for the maximum likelihood solution (rank 1)
plotAbs(purecn.example.output, 1, type="hist")
plotAbs(purecn.example.output, 1, type="BAF")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PureCN/plotAbs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotAbs
> ### Title: Plots for analyzing PureCN solutions
> ### Aliases: plotAbs
> 
> ### ** Examples
> 
> data(purecn.example.output)
> plotAbs(purecn.example.output, type="overview")
> # plot details for the maximum likelihood solution (rank 1)
> plotAbs(purecn.example.output, 1, type="hist")
> plotAbs(purecn.example.output, 1, type="BAF")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>