HMMcopy (version 1.14.0)

HMMcopy Visualization: Visualization functions for correctReadcount results

Description

Convinience functions for creating plots for the analysis of the readcount correction process by correctReadcount

Usage

plotBias(correctOutput, points = 10000, ...)
plotCorrection(correctOutput, chr = space(correctOutput)[1], ...)
plotSegments(correctOutput, segmentOutput, chr = space(correctOutput)[1], ...)
plotParam(segmentOutput, param, ...)
stateCols()

Arguments

correctOutput

Output value from correctReadcount

segmentOutput

Output value from HMMsegment

points

Number of random sampled points to plot, decreasing reduces runtime

chr

Chromosome name to plot. A single value for plotCorrection and a vector for plotSegments.

param

Input parameters to call that produced segmentOutput

...

Furthur arguments are passed to plot.

Details

plotBias shows the effects of the correction process on GC bias and mappability bias in HTS readcounts.

plotCorrection shows the effects of the correction on the copy number profile. Defaultly plotting the entire first chromosome found in the list.

plotSegments shows the resultant segments and states assigned to each segment.

plotParam shows the initial suggested distribution of copy number in each state (dashed), and the optimal distribution of copy number in each state (solid)

stateCols returns a vector of six colours used in plotSegments and plotParam

See Also

correctReadcount and HMMsegment for generating intended output.

Examples

data(tumour)

# Visualize one at a time
par(ask = TRUE)
plotBias(normal_copy)
plotCorrection(tumour_copy)
par(mfrow = c(1, 1))
plotSegments(tumour_copy, tumour_segments)
plotParam(tumour_segments, tumour_param)