plotBoxplot: Create box plot of normalized read counts
In panelcn.mops: CNV detection tool for targeted NGS panel data

Description Usage Arguments Value Examples

Create box plot of normalized read counts

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plotBoxplot(result, sampleName, countWindows, selectedGenes = NULL,
  showGene = 1, showLegend = TRUE, exonRange = NULL, ylimup = 1.15,
  thresh = 0)

`result`	result object of panelcn.mops
`sampleName`	name of the test sample that should be displayed
`countWindows`	data.frame with contents of a BED file as returned by getWindows
`selectedGenes`	vector of names of genes of interest that should be displayed or NULL if all genes are of interest. Default = NULL
`showGene`	integer indicating which of the genes of interest to plot
`showLegend`	flag to indicate whether to display a legend with the names of the test samples. Default = TRUE
`exonRange`	vector of 2 positive integers to limit box plot to a certain range of exons or NULL
`ylimup`	numeric, maximum RC is multiplied by this value to calculate second value of ylim. Default = 1.15
`thresh`	numeric threshold for plotting fold change areas E.g. thresh = 0.4 plots a green rectangle above (1 + 0.4)median for each boxplot and a red rectangle below (1 - 0.4)median. Default of zero does not plot any colored areas.

generates a boxplot of the normalized read counts

data(panelcn.mops)
sampleNames <- colnames(elementMetadata(test))
selectedGenes <- "ATM"
plotBoxplot(result = resultlist[[1]], sampleName = sampleNames[1], 
            countWindows = countWindows, selectedGenes = selectedGenes, 
            showGene = 1)

Loading required package: cn.mops
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: ‘cn.mops’

The following object is masked from ‘package:S4Vectors’:

    params