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

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

Author(s)

Daniel Lai

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(HMMcopy)
Loading required package: IRanges
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: geneplotter
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: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/HMMcopy/HMMcopy-visualize.Rd_%03d_medium.png", width=480, height=480)
> ### Name: HMMcopy Visualization
> ### Title: Visualization functions for correctReadcount results
> ### Aliases: plotBias plotCorrection plotParam plotSegments stateCols
> ### Keywords: hplot
> 
> ### ** 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)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>