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Last data update: 2014.03.03

R: Auxiliary functions to create comparitive Figures

affycomp.compfigs.auxiliary

R Documentation

Auxiliary functions to create comparitive Figures

Description

These functions are auxiliary function to affycompPlot. These Figures are used to compare expression measures. They take lists with components created by the assessDilution and assessSpikeIn functions.

Usage

affycomp.compfig2(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 2")

affycomp.compfig3(l, method.names = as.character(1:length(l)),
                  main = "Figure 3")

affycomp.compfig4a(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, main = "Figure 4a")

affycomp.compfig4b(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, main = "Figure 4b")

affycomp.compfig4c(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, rotate=TRUE, main = "Figure 4c")

affycomp.compfig5a(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5a", maxfp=100)

affycomp.compfig5b(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5b", maxfp=100)

affycomp.compfig5cde(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5c", maxfp=100,
                  type=c("low","med","high"))

affycomp.compfig5c(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5c", maxfp=100)

affycomp.compfig5d(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5d", maxfp=100)

affycomp.compfig5e(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5e", maxfp=100)

Arguments

`l`	a list of lists with the necessary components to create the Figure. See details.
`method.names`	a character vector with the names of the expression measures methodologies being compared.
`add.legend`	logical. If TRUE a legend is added.
`main`	title of the Figure.
`rotate`	in the case of compfig4c one can eiher show the actual local slopes or the bias (local slope minus 1).
`maxfp`	range of the false positives in ROC will be from 0 to `maxfp`
`type`	compfig5cdef is the engine for 5c, 5d, and 5e. `type` tells is which of these 4 to run.

Details

These are similar to the functions defined in affycomp.figures.auxiliary. Main difference is that here you send lists with the result of the assessment functions as components.

Value

Figures are produced.

Author(s)

Rafael A. Irizarry

Examples

library(affycompData)
data(rma.assessment)
data(mas5.assessment)
affycomp.compfig2(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig3(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig4a(list(rma.assessment$Signal,mas5.assessment$Signal))
affycomp.compfig4b(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig5a(list(rma.assessment$FC,mas5.assessment$FC))
affycomp.compfig5b(list(rma.assessment$FC2,mas5.assessment$FC2))

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(affycomp)
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/affycomp/affycomp.compfigs.auxiliary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: affycomp.compfigs.auxiliary
> ### Title: Auxiliary functions to create comparitive Figures
> ### Aliases: affycomp.compfigs.auxiliary affycomp.compfig2
> ###   affycomp.compfig2b affycomp.compfig3 affycomp.compfig4a
> ###   affycomp.compfig4b affycomp.compfig4c affycomp.compfig5a
> ###   affycomp.compfig5b affycomp.compfig5cde affycomp.compfig5c
> ###   affycomp.compfig5d affycomp.compfig5e
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library(affycompData)
> data(rma.assessment)
> data(mas5.assessment)
> affycomp.compfig2(list(rma.assessment$Dilution,mas5.assessment$Dilution))
> affycomp.compfig3(list(rma.assessment$Dilution,mas5.assessment$Dilution))
> affycomp.compfig4a(list(rma.assessment$Signal,mas5.assessment$Signal))
> affycomp.compfig4b(list(rma.assessment$Dilution,mas5.assessment$Dilution))
> affycomp.compfig5a(list(rma.assessment$FC,mas5.assessment$FC))
> affycomp.compfig5b(list(rma.assessment$FC2,mas5.assessment$FC2))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>