chromIntensityPlot: Plot B Allele Frequency and/or Log R Ratio, R or Theta values...
In GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Author(s) See Also Examples

This function creates plots for one or more of the 'B AlleleFreq', 'Log R Ratio', 'R' or 'Theta' values for given sample by chromosome combinations.

chromIntensityPlot(intenData, scan.ids, chrom.ids, 
  type = c("BAF/LRR", "BAF", "LRR", "R", "Theta", "R/Theta"), 
  main = NULL, info = NULL, abln = NULL,
  horizln = c(1/2, 1/3, 2/3), 
  colorGenotypes = FALSE, genoData = NULL,
  colorBatch = FALSE, batch.column = NULL,
  snp.exclude = NULL,
  ideogram=TRUE, ideo.zoom=TRUE, ideo.rect=FALSE,
  cex=0.5, cex.leg=1.5, 
  colors = c("default", "neon", "primary"), ...)

`intenData`	`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`.

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).

Caitlin McHugh, Cathy Laurie

IntensityData, GenotypeData, BAFfromGenotypes

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)

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, 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

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