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Last data update: 2014.03.03

R: Genomic reports

GenomicReports

R Documentation

Genomic reports

Description

Create reports for all samples in a dataset.

Usage

reportChromosomesSmoothCopyNumber(snpdata, grouping, normalizedTo=2, 
  smooth.lambda=2, ridge.kappa=0, plotLOH=c("none", "marker", "line", "NorTum"), 
  sample.colors = NULL, ideo.bleach=0.25, ...)
reportSamplesSmoothCopyNumber(snpdata, grouping, normalizedTo=2, 
  smooth.lambda=2, ridge.kappa=0, plotLOH=c("none", "marker", "line", "NorTum"), 
  sample.colors=NULL, ...)
reportGenomeGainLossLOH(snpdata, grouping, plotSampleNames=FALSE, sizeSampleNames=4, 
  distance.min, upcolor="red", downcolor="blue", lohcolor="grey", hetcolor="lightgrey", 
  lohwidth=1, segment=101, orientation=c("V","H"), ...)
reportChromosomeGainLossLOH(snpdata, grouping, plotSampleNames=FALSE, distance.min,
  upcolor="red", downcolor="blue", lohcolor="grey", hetcolor="lightgrey", proportion=0.2, 
  plotLOH=TRUE, segment=101, ...)
reportGenomeIntensityPlot(snpdata, normalizedTo=NULL, subsample=NULL, smoothing=c("mean", "quant"),
  dot.col="black", smooth.col="red", ...)

Arguments

`snpdata`	SnpSetIllumina object.
`grouping`	factor, elements with same value are plotted together. Defaults to groups of 4 in order of the samples in the object.
`normalizedTo`	numeric, a horizontal line is drawn at this position.
`smooth.lambda`	smoothing parameter for `quantsmooth`.
`ridge.kappa`	smoothing parameter for `quantsmooth`.
`plotLOH`	indicate regions or probes with LOH, see details.
`sample.colors`	vector of color.
`plotSampleNames`	logical.
`sizeSampleNames`	numeric, margin size for sample names.
`distance.min`	numerical.
`upcolor`	color.
`downcolor`	color.
`lohcolor`	color.
`hetcolor`	color.
`lohwidth`	numerical, relative width of the LOH part of the sample
`segment`	integer.
`orientation`	["V","H"], vertical or horizontal orientation of plot.
`proportion`	numerical, proportion of the plot to use for idiogram annotation
`subsample`	character, or factor of length of features
`smoothing`	Type of smoothing per chromosome.
`dot.col`	color.
`smooth.col`	color.
`ideo.bleach`	numeric [0,1]
`...`	arguments are forwarded to `plot` or `getChangedRegions`.

Details

The first function creates plots for each group and each chromosome in the dataset. The second function creates full genome plot for each group in the dataset. Beware that a lot of plots can be created, and usually you should prepare for that, by redirecting the plots to pdf or functions that create picture files like jpg, png, bmp.

Value

These functions are executed for their side effects

Author(s)

Jan Oosting

Examples

data(chr17.260)
chr17nrm <- standardNormalization(chr17.260)
par(mfrow = c(4,2), mar = c(2,4,2,1))
reportChromosomesSmoothCopyNumber(chr17nrm, grouping=pData(chr17.260)$Group,smooth.lambda = 4)

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(beadarraySNP)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: quantsmooth
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarraySNP/GenomicReports.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GenomicReports
> ### Title: Genomic reports
> ### Aliases: reportChromosomesSmoothCopyNumber
> ###   reportSamplesSmoothCopyNumber reportGenomeGainLossLOH
> ###   reportChromosomeGainLossLOH reportGenomeIntensityPlot
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(chr17.260)
> chr17nrm <- standardNormalization(chr17.260)
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

> par(mfrow = c(4,2), mar = c(2,4,2,1))
> reportChromosomesSmoothCopyNumber(chr17nrm, grouping=pData(chr17.260)$Group,smooth.lambda = 4)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>