copynumber (version 1.12.0)

plotAllele: Plot SNP data and/or aspcf segmentation results

Description

Plot bivariate SNP data and/or aspcf segmentation results for each sample separately with chromosomes in different panels

Usage

plotAllele(logR = NULL, BAF = NULL, segments = NULL, pos.unit = "bp", 
            sample = NULL, chrom = NULL, assembly="hg19", baf.thres = 
            c(0.1,0.9), winsoutliers = NULL, xaxis = "pos", layout = c(1,1), 
            plot.ideo = TRUE, ...)

Arguments

logR

a data frame with numeric or character chromosome numbers in the first column, numeric local probe positions in the second, and numeric copy number data for one or more samples in subsequent columns. The header of the copy number column(s) should give the sample IDss.

BAF

a data frame on the same format and size as logR, with chromosomes and local probe positions in the two first columns, and numeric BAF-measurements for one or more samples in subsequent columns.

segments

a data frame or a list of data frames containing the segmentation results found by aspcf.

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".

sample

a numeric vector indicating which sample(s) is (are) to be plotted. The number(s) should correspond to the sample's place (in order of appearance) in logR, or in segments if logR is unspecified.

chrom

a numeric or character vector with chromosome number(s) to indicate which chromosome(s) is (are) to be plotted.

assembly

a string specifying which genome assembly version should be applied to define the chromosome ideogram. Allowed options are "hg19", "hg18", "hg17" and "hg16" (corresponding to the four latest human genome annotations in the UCSC genome browser).

baf.thres

a numeric vector of length 2 giving thresholds below/above which BAF-values will not be plotted (use this to remove germline homozygous BAF probes from the plot).

winsoutliers

an optional data frame of the same size as logR identifying observations classified as outliers by winsorize. If specified, outliers will be marked by a different color and symbol than the other observations (see wins.col and wins.pch).

xaxis

either "pos" or "index". The former implies that the xaxis will represent the genomic positions, whereas the latter implies that the xaxis will represent the probe indices. Default is "pos".

layout

an integer vector of length two giving the number of rows and columns in the plot. Default is c(1,1).

plot.ideo

a logical value indicating whether the chromosome ideogram should be plotted. Only applicable when xaxis="pos".

...

other graphical parameters. These include the common plot arguments xlab, ylab, main, xlim, ylim, col (default is "grey"), pch (default is 46, equivalent to "."), cex, cex.lab, cex.main, cex.axis, las, tcl, mar and mgp (see par on these). In addition, a range of graphical arguments specific for copy number plots may be specified, see plotSample on these.

Details

Several chromosome may be displayed on the same page with the layout option. If the number of chromosomes exceeds the desired page layout, the user is prompted before advancing to the next page of output.

Examples

#Load logR and BAF data:
data(logR)
data(BAF)

#Run aspcf::
aspcf.segments <- aspcf(logR,BAF)

#Plot
plotAllele(logR,BAF,aspcf.segments,layout=c(2,2))