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Last data update: 2014.03.03

R: Plot percentage of samples with an aberration at a genomic...

plotFreq

R Documentation

Plot percentage of samples with an aberration at a genomic position

Description

Plot the percentage of samples that have an amplification or deletion at a genomic position. Amplifications/deletions correspond to copy number values that are above/below a pre-defined threshold. Frequencies may be plotted over the entire genome or separately for each chromosome.

Usage

plotFreq(segments, thres.gain, thres.loss = -thres.gain, pos.unit = "bp", 
    chrom = NULL, layout = c(1, 1),...)

Arguments

`segments`	a data frame containing the segmentation results found by either `pcf` or `multipcf`.
`thres.gain`	a numeric vector giving the threshold value(s) to be applied for calling gains.
`thres.loss`	a numeric vector of same length as `thres.gain` giving the threshold value(s) to be applied for calling losses. Default is to use the negative value of `thres.gain`.
`pos.unit`	the unit used to represent the probe positions. Allowed options are "mbp" (mega base pairs), "kbp" (kilo base pairs) or "bp" (base pairs). By default assumed to be "bp".
`chrom`	a numeric or character vector with chromosome number(s) to indicate which chromosome(s) is (are) to be plotted. If unspecified the whole genome is plotted, otherwise each specified chromosome is plotted in a separate panel.
`layout`	an integer vector of length two giving the number of rows and columns in the plot. Default is `c(1,1)`.
`...`	other graphical parameters. These include the common plot arguments `xlab`, `ylab`, `title`, `main`, `cex.main`, `mgp`, `cex.lab`, `cex.axis`, `ylim`, `xlim`, and `las` (see `par` on these), as well as `plot.size`, `plot.unit`, `plot.ideo`, `ideo.frac`, `cyto.text`, `assembly` and `cex.cytotext` (see `plotSample` on these). In addition, some other graphical arguments specific for this plot function may be specified: `col.gain` the color to be used for the gain frequencies, default is "red". `col.loss` the color to be used for the loss frequencies, default is "blue". `continuous` a logical value indicating whether the probe frequencies should be presented as continuous, i.e. the plotted probe frequency will start and end halfway between adjacent probes (except across arms when chromosomes are plotted and except across chromosomes when genome is plotted). Default is TRUE. `percentLines` either a logical value indicating if horizontal percentages lines should be plotted, or a numeric vector with percentages at which such lines should be plotted. Default is TRUE.

Details

The percentage of samples with an aberration is calculated and plotted for all genomic positions. Regions with gain or loss will be those where copy number values are above or below the values given in thres.gain and thres.loss, respectively.

Note

This function applies par(fig), and is therefore not compatible with other setups for arranging multiple plots in one device such as par(mfrow,mfcol).

Author(s)

Gro Nilsen

Examples

#load lymphoma data
data(lymphoma)
#Run pcf
seg <- pcf(data=lymphoma,gamma=12)

#Plot over entire genome, gain and loss thresholds are 0.1 and -0.1:
plotFreq(segments=seg,thres.gain=0.1)

#Plot by chromosomes, two sets of thresholds:
plotFreq(segments=seg,thres.gain=c(0.1,0.2), thres.loss=c(-0.05,-0.1), chrom=c(1:23),
layout=c(5,5))

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(copynumber)
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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/copynumber/plotFreq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotFreq
> ### Title: Plot percentage of samples with an aberration at a genomic
> ###   position
> ### Aliases: plotFreq
> 
> ### ** Examples
> 
> #load lymphoma data
> data(lymphoma)
> #Run pcf
> seg <- pcf(data=lymphoma,gamma=12)
pcf finished for chromosome arm 1p 
pcf finished for chromosome arm 1q 
pcf finished for chromosome arm 2p 
pcf finished for chromosome arm 2q 
pcf finished for chromosome arm 3p 
pcf finished for chromosome arm 3q 
pcf finished for chromosome arm 4p 
pcf finished for chromosome arm 4q 
pcf finished for chromosome arm 5p 
pcf finished for chromosome arm 5q 
pcf finished for chromosome arm 6p 
pcf finished for chromosome arm 6q 
pcf finished for chromosome arm 7p 
pcf finished for chromosome arm 7q 
pcf finished for chromosome arm 8p 
pcf finished for chromosome arm 8q 
pcf finished for chromosome arm 9p 
pcf finished for chromosome arm 9q 
pcf finished for chromosome arm 10p 
pcf finished for chromosome arm 10q 
pcf finished for chromosome arm 11p 
pcf finished for chromosome arm 11q 
pcf finished for chromosome arm 12p 
pcf finished for chromosome arm 12q 
pcf finished for chromosome arm 13q 
pcf finished for chromosome arm 14q 
pcf finished for chromosome arm 15q 
pcf finished for chromosome arm 16p 
pcf finished for chromosome arm 16q 
pcf finished for chromosome arm 17p 
pcf finished for chromosome arm 17q 
pcf finished for chromosome arm 18p 
pcf finished for chromosome arm 18q 
pcf finished for chromosome arm 19p 
pcf finished for chromosome arm 19q 
pcf finished for chromosome arm 20p 
pcf finished for chromosome arm 20q 
pcf finished for chromosome arm 21q 
pcf finished for chromosome arm 22q 
pcf finished for chromosome arm 23p 
pcf finished for chromosome arm 23q 
> 
> #Plot over entire genome, gain and loss thresholds are 0.1 and -0.1:
> plotFreq(segments=seg,thres.gain=0.1)
> 
> #Plot by chromosomes, two sets of thresholds:
> plotFreq(segments=seg,thres.gain=c(0.1,0.2), thres.loss=c(-0.05,-0.1), chrom=c(1:23),
+ layout=c(5,5))
>   
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>