getting p-values from two dataframes

t.test.p.values.R

#read MAOA and MAOB human RNAseq data and use t.test by regions
setwd("/home/mydirectory/work.dir/allen.brain/human")
maoa = read.csv("combinedA.csv")
maob = read.csv("combinedB.csv")
test.result = mapply(t.test, maoa, maob)

#store p-values by brain region:
#p.values = mapply(function(x, y) t.test(x,y)$p.value, maoa, maob)

#store p-values in a column with regions in a separate column:
p.values = stack(mapply(function(x, y) t.test(x,y)$p.value, maoa, maob))

#order p-values
ordered = p.values[with(p.values, order(values)),]

#make a heatmap
matrix.maoa = as.matrix(maoa)
matrix.maob = as.matrix(maob)

fun = Vectorize(function(i,j) t.test(matrix.maoa[,i],matrix.maob[,j])$p.value)
res = outer(1:169,1:169,FUN = "fun")

image(1:169,1:169,res,axes=FALSE,xlab="MAOA",ylab="MAOB")
axis(1, at = 1:169,labels=colnames(maoa))
axis(2, at = 1:169,labels=colnames(maoa))

#TOP REGIONS OF HUMAN DIFFERENTIAL EXPRESSION
#Central Nucleus
#VIIIB
#Crus II
#middle frontal gyrus
#III
#Anterior group of nuclei
#precuneus
#pontine raphe nucleus
#Supramammillary nucleus
#VI
#Inferior occipital gyrus
#central glial substance
#CA4 field
#Paraventricular Nuclei of Thalamus
#Ventromedial hypothalamic nucleus
#Posterior group of nuclei
#Tuberomammillary nucleus
#Perifornical nucleus
#central grey substance of midbrain