IntensityData object, must contain at least one of 'BAlleleFreq', 'LogRRatio', 'X', 'Y'.
scan.ids
A vector containing the scan IDs to plot.
chrom.ids
A vector containing the chromosomes to plot for each
scanID (should have same length as scan.ids).
type
The type of plot to be created. 'BAF/LRR' creates both 'B Allele Freq' and 'Log R Ratio' plots. 'R/Theta' creates both 'R' and 'Theta' plots.
main
Vector of plot titles. If NULL then the title will
include scanID, sex, and chromosome.
info
A character vector containing extra information to include in the main title.
abln
A vector of values that is of length 2*length(scan.ids). Each pair of entries specifies where vertical lines will be drawn in each plot.
This is especially useful when drawing the start & end breakpoints for anomalies, for example.
Use -1 as one pair value for plots that warrant only one line. By default, no lines will be drawn.
horizln
A vector containing the y-axis values at which a horizontal line will be drawn in B Allele Frequency plots.
colorGenotypes
A logical value specifying whether to color-code
the points by called genotype. if TRUE, genoData must be given also.
genoData
GenotypeData object, required if colorGenotypes=TRUE.
colorBatch
A logical value specifying whether to color-code the
points by sample batch (e.g, plate). If TRUE, batch.column must also
be specified.
batch.column
A character string indicating which annotation
variable in intenData should be used as the batch.
snp.exclude
An integer vector giving the IDs of SNPs to exclude
from the plot.
ideogram
logical for whether to plot a chromosome ideogram under
the BAF and LRR plots.
ideo.zoom
logical for whether to zoom in on the ideogram to
match the range of the BAF/LRR plots.
ideo.rect
logical for whether to draw a rectangle on the
ideogram indicating the range of the BAF/LRR plots.
cex
cex value for points on the plots.
cex.leg
cex value for the ideogram legend.
colors
Color scheme to use for genotypes. "default" is colorblind safe (colorbrewer Set2), "neon" is bright orange/green/fuschia, and "primary" is red/green/blue.
...
Other parameters to be passed directly to plot.
Details
For all plots, a vertical line is drawn every one eigth of the
chromosome. For the Log R Ratio plot, the y-axis has been given the range of (-2,2).
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(GWASTools)
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")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/chromIntensityPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chromIntensityPlot
> ### Title: Plot B Allele Frequency and/or Log R Ratio, R or Theta values
> ### for samples by probe position on a chromosome
> ### Aliases: chromIntensityPlot
> ### Keywords: hplot
>
> ### ** Examples
>
> library(GWASdata)
> data(illuminaScanADF)
>
> blfile <- system.file("extdata", "illumina_bl.gds", package="GWASdata")
> bl <- GdsIntensityReader(blfile)
> intenData <- IntensityData(bl, scanAnnot=illuminaScanADF)
>
> genofile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
> geno <- GdsGenotypeReader(genofile)
> genoData <- GenotypeData(geno, scanAnnot=illuminaScanADF)
>
> scanID <- getScanID(illuminaScanADF, index=1)
> chromIntensityPlot(intenData=intenData, scan.ids=scanID,
+ chrom.ids=22, type="BAF/LRR", info="interesting sample",
+ colorGenotypes=TRUE, genoData=genoData)
> close(genoData)
> close(intenData)
>
>
>
>
>
> dev.off()
null device
1
>