massi_y_plot

Description

The massi_y_plot function plots the data output from massi.y function.

Usage

massi_y_plot(massi_y_out)

Arguments

Details

This function produces a bar plot of the coefficient of variation (CV) for each probe in the dataset. This allows the user to identify the most variable probes that are likely to be the most informative in the sex prediction step. The 25%, 50% and 75% quantiles are represented as horizontal lines and represent the threshold values that can be specified for the massi_select function.

Value

This function produces a bar plot in a new graphics device.

Note

See vignette for more details.

Author(s)

Sam Buckberry

See Also

massi_y, massi_select, massi_cluster, massi_dip, massi_cluster_plot

Examples

data(massi.test.dataset, massi.test.probes)

massi_y_out <-
  massi_y(expression_data=massi.test.dataset, y_probes=massi.test.probes)
  
massi_y_plot(massi_y_out)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(massiR)
Loading required package: cluster
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: diptest
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/massiR/massi_y_plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: massi_y_plot
> ### Title: massi_y_plot
> ### Aliases: massi_y_plot
> 
> ### ** Examples
> 
> 
> data(massi.test.dataset, massi.test.probes)
> 
> massi_y_out <-
+   massi_y(expression_data=massi.test.dataset, y_probes=massi.test.probes)
>   
> massi_y_plot(massi_y_out)
Error in dev.new() : no suitable unused file name for pdf()
Calls: massi_y_plot -> dev.new
Execution halted