PureCN (version 1.0.3)

plotAbs: 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

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")