plots4epheno: Summary plots for gene signature vs phenotype association

In phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

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

x	epheno object, as returned by ExpressionPhenoTest.
signatures	List with each element corresponding to a signature. The gene names in each signature must match those in epheno.
referenceSignature	If specified, the average fold change in each signature is compared to the average fold change in the signature referenceSignature.
testUpDown	If set to TRUE, bars corresponding to up and down-regulated genes are compared with those of referenceSignature separately. This argument is ignored if referenceSignature is not specified.
cex.text	Character expansion for the text indicating the P-values. Ignored if referenceSignature is missing.
alpha	Confidence levels for barplot error bars.
p.adjust.method	P-value adjustment method, passed on to p.adjust.
simulate.p.value	A logical indicating whether chi-square p-values should be computed by Monte Carlo simulation (passed on to chisq.test).
B	Integer specifying the number of replicates in the Monte Carlo simulation (passed on to chisq.test).
ylab	y-axis labels
ylim	y-axis limits
...	Other arguments to be passed on to boxplot.

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)

phenoTest documentation built on Nov. 8, 2020, 7:53 p.m.