plotCompareP {variancePartition}R Documentation

Compare p-values from two analyses

Description

Plot -log10 p-values from two analyses and color based on donor component from variancePartition analysis

Usage

plotCompareP(p1, p2, vpDonor, dupcorvalue, fraction = 0.2,
  xlabel = bquote(duplicateCorrelation ~ (-log[10] ~ p)),
  ylabel = bquote(dream ~ (-log[10] ~ p)))

Arguments

p1

p-value from first analysis

p2

p-value from second analysis

vpDonor

donor component for each gene from variancePartition analysis

dupcorvalue

scalar donor component from duplicateCorrelation

fraction

fraction of highest/lowest values to use for best fit lines

xlabel

for x-axis

ylabel

label for y-axis

Value

ggplot2 plot

Examples


# load library
# library(variancePartition)

# optional step to run analysis in parallel on multicore machines
# Here, we used 4 threads
library(doParallel)
cl <- makeCluster(4)
registerDoParallel(cl)
# or by using the doSNOW package

# load simulated data:
# geneExpr: matrix of gene expression values
# info: information/metadata about each sample
data(varPartData)

# Perform very simple analysis for demonstration

# Analysis 1
form <- ~ Batch 
L = getContrast( geneExpr, form, info, "Batch3")
fit = dream( geneExpr, form, info, L)
fitEB = eBayes( fit )
res = topTable( fitEB, number=Inf )

# Analysis 2
form <- ~ Batch + (1|Tissue)
L = getContrast( geneExpr, form, info, "Batch3")
fit = dream( geneExpr, form, info, L)
fitEB = eBayes( fit )
res2 = topTable( fitEB, number=Inf )

# Compare p-values
plotCompareP( res$P.Value, res2$P.Value, runif(nrow(res)), .3 )

# stop cluster
stopCluster(cl)


[Package variancePartition version 1.10.4 Index]