Summary plots for gene signature vs phenotype association

Description

Summarizes the univariate relationships between genes in one or more signatures and several phenotype variables, as summarized in epheno objects (which can be created with the ExpressionPhenoTest function).

By default barplotSignifSignatures performs a binomial test (binom.test from package stats) for each signature to see if the number of up up regulated and down regulated genes is different enough to be statistically different. When a reference gene set is provided we test if the proportions of up and down regulated genes of each gene set is different from the proportions in the reference gene set. This has been done with a chi-square test. When a reference gene set is provided and parameter testUpDown is TRUE (by default its FALSE) the number of genes corresponding to up and down regulated are compared with those of the reference gene set separately.

Usage

barplotSignatures(x, signatures, referenceSignature, alpha=.05,
p.adjust.method='none', ylab, cex.text=1, ...)
barplotSignifSignatures(x, signatures, referenceSignature, testUpDown=FALSE,
simulate.p.value = FALSE, B = 10^4, p.adjust.method='none', alpha=.05,
ylab, ylim=ylim, cex.text=1, ...)

Arguments

Value

When a single signature is provided as input, a single plot assessing the association of that signature with all phenotype variables is created. If several signatures are provided, one separate plot is created for each phenotype variable.

Author(s)

Evarist Planet

Examples

#create epheno
data(epheno)

#construct two signatures
sign1 <- sample(featureNames(epheno))[1:20]
sign2 <- sample(featureNames(epheno))[1:15]
mySignature <- list(sign1,sign2)
names(mySignature) <- c('My first signature','My preferred signature')

#plot
barplotSignifSignatures(epheno[,'Relapse'],mySignature,alpha=0.05)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(phenoTest)
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")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: Heatplus
Loading required package: BMA
Loading required package: survival
Loading required package: leaps
Loading required package: robustbase

Attaching package: 'robustbase'

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

    heart

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

    rowMedians

Loading required package: inline
Loading required package: rrcov
Scalable Robust Estimators with High Breakdown Point (version 1.3-11)

Loading required package: ggplot2

/////////////////////////////////////////////////////////////////////////////

//------------------    Thanks for using HTSanalyzeR    -------------------//
 
//------------please use function changes() to see new changes-------------//

//------------please report any bug to xinwang2hms@gmail.com---------------//

/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/phenoTest/plots4epheno.Rd_%03d_medium.png", width=480, height=480)
> ### Name: barplotSignatures
> ### Title: Summary plots for gene signature vs phenotype association
> ### Aliases: barplotSignatures barplotSignifSignatures
> ### Keywords: graph
> 
> ### ** Examples
> 
> #create epheno
> data(epheno)
> 
> #construct two signatures
> sign1 <- sample(featureNames(epheno))[1:20]
> sign2 <- sample(featureNames(epheno))[1:15]
> mySignature <- list(sign1,sign2)
> names(mySignature) <- c('My first signature','My preferred signature')
> 
> #plot
> barplotSignifSignatures(epheno[,'Relapse'],mySignature,alpha=0.05)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>