plot LinkVariantAlmlof objects

Description

plot an object of type LinkVariantAlmlof

Usage

plot(x, y, ...)

## S4 method for signature 'LinkVariantAlmlof,ANY'
plot(x, y, ...)

Arguments

Author(s)

Jesper R. Gadin, Lasse Folkersen

Examples

data(ASEset) 
a <- ASEset
# Add phase
set.seed(1)
p1 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
p2 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
p <- matrix(paste(p1,sample(c("|","|","/"), size=nrow(a)*ncol(a), replace=TRUE), p2, sep=""),
	nrow=nrow(a), ncol(a))

phase(a) <- p

#add alternative allele information
mcols(a)[["alt"]] <- inferAltAllele(a)

#init risk variants
p.ar <- phaseMatrix2Array(p)
rv <- RiskVariantFromGRangesAndPhaseArray(x=GRvariants, phase=p.ar)

#colnames has to be samea and same order in ASEset and RiskVariant
colnames(a) <- colnames(rv)

# in this example each and every snp in the ASEset defines a region
r1 <- granges(a)

# in this example two overlapping subsets of snps in the ASEset defines the region
r2 <- split(granges(a)[c(1,2,2,3)],c(1,1,2,2))

# link variant almlof (lva)
lv1 <- lva(a, rv, r1)
lv2 <- lva(a, rv, r2)
plot(lv2[1])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(AllelicImbalance)
Loading required package: grid
Loading required package: GenomicRanges
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AllelicImbalance/LinkVariantAlmlof-plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LinkVariantAlmlof-plot
> ### Title: plot LinkVariantAlmlof objects
> ### Aliases: LinkVariantAlmlof-plot plot plot,LinkVariantAlmlof,ANY-method
> ###   plot,LinkVariantAlmlof-method
> ### Keywords: plot
> 
> ### ** Examples
> 
> 
> data(ASEset) 
> a <- ASEset
> # Add phase
> set.seed(1)
> p1 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
> p2 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
> p <- matrix(paste(p1,sample(c("|","|","/"), size=nrow(a)*ncol(a), replace=TRUE), p2, sep=""),
+ 	nrow=nrow(a), ncol(a))
> 
> phase(a) <- p
> 
> #add alternative allele information
> mcols(a)[["alt"]] <- inferAltAllele(a)
> 
> #init risk variants
> p.ar <- phaseMatrix2Array(p)
> rv <- RiskVariantFromGRangesAndPhaseArray(x=GRvariants, phase=p.ar)
> 
> #colnames has to be samea and same order in ASEset and RiskVariant
> colnames(a) <- colnames(rv)
> 
> # in this example each and every snp in the ASEset defines a region
> r1 <- granges(a)
> 
> # in this example two overlapping subsets of snps in the ASEset defines the region
> r2 <- split(granges(a)[c(1,2,2,3)],c(1,1,2,2))
> 
> # link variant almlof (lva)
> lv1 <- lva(a, rv, r1)
> lv2 <- lva(a, rv, r2)
> plot(lv2[1])
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>