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Last data update: 2014.03.03

R: SNP correlation plot

snpCorrelationPlot

R Documentation

SNP correlation plot

Description

Plots SNP correlation versus chromosome.

Usage

snpCorrelationPlot(correlations, chromosome, 
                   ylim=c(0,1), ylab = "abs(correlation)", ...)

Arguments

`correlations`	A vector of correlations.
`chromosome`	A vector containing the chromosome for each SNP.
`ylim`	The limits of the y axis.
`ylab`	The label for the y axis.
`...`	Other parameters to be passed directly to `plot`.

Details

Plots SNP correlations (from, e.g., PCA), versus chromosome.

correlations must have the same length as chromosome and is assumed to be in order of position on each chromosome. Values within each chromosome are evenly spaced along the X axis.

Author(s)

Cathy Laurie

Examples

correlations <- sample(0.001*(0:1000), 1000, replace=TRUE)
chromosome <- c(rep(1,400), rep(2,350), rep("X",200), rep("Y",50))
snpCorrelationPlot(correlations, chromosome)

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> 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/snpCorrelationPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snpCorrelationPlot
> ### Title: SNP correlation plot
> ### Aliases: snpCorrelationPlot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> correlations <- sample(0.001*(0:1000), 1000, replace=TRUE)
> chromosome <- c(rep(1,400), rep(2,350), rep("X",200), rep("Y",50))
> snpCorrelationPlot(correlations, chromosome)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>