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Last data update: 2014.03.03

R: display the association between expression values and...

plot_EvG

R Documentation

display the association between expression values and genotypes in an smlSet instance

Description

display the association between expression values and genotypes in an smlSet instance

Usage

plot_EvG(gsym, rsid, sms, ...)

Arguments

`gsym`	instance of class `genesym` or `probeId`, casting a string that names a gene (which will be looked up using the `annotation` slot of `sms`) or a probe which must be resident on the array underlying the expression content of `sms`
`rsid`	instance of class `rsid` naming a SNP with genotype values given among the columns of the `smList` components of `sms`
`sms`	an instance of `smlSet`
`...`	additional parameter to `plot`

Details

When the genotype is categorical, will use boxplots; when genotype has been imputed and includes expected allele counts, will use a scatterplot.

Value

a plot is rendered on the current display

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Examples

 if ("GGtools" %in% installed.packages()[,1]) {
  s20 = getSS("GGtools", "20")
  plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
 }

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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> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGBase/plot_EvG.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_EvG
> ### Title: display the association between expression values and genotypes
> ###   in an smlSet instance
> ### Aliases: plot_EvG plot_EvG,genesym,rsid,smlSet-method
> ###   plot_EvG,probeId,rsid,smlSet-method
> ### Keywords: models
> 
> ### ** Examples
> 
>  if ("GGtools" %in% installed.packages()[,1]) {
+   s20 = getSS("GGtools", "20")
+   plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
+  }

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")'.


Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand, rowMeans, rowSums

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

    colMeans, colSums, expand.grid, rowMeans, rowSums



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