RRHO2: RRHO2
In Caleb-Huo/RRHO2: improved RRHO package

Description Usage Arguments Details Value Author(s) Examples

An improved version for RRHO, which aims to correct the intepretation for top left region (up in x and down in y) nad bottom right region.

1 2	RRHO2(list1, list2, stepsize = defaultStepSize(list1, list2), labels, plots = FALSE, outputdir = NULL, BY = FALSE, log10.ind = FALSE)

`list1`	data.frame. First column is the element (possibly gene) identifier, and the second is its value on which to sort. For differential gene expression, values are often -log10(P-value) * sign(effect).
`list2`	data.frame. Same as list1.
`stepsize`	Controls the resolution of the test: how many items between any two overlap tests.
`labels`	Character vector with two elements: the labels of the two lists.
`plots`	Logical. Should output plots be returned?
`outputdir`	Path name where plots ae returned.
`BY`	Logical. Should Benjamini-Yekutieli FDR corrected pvalues be computed?
`log10.ind`	Logical. Should pvalues be reported and plotted in -log10 scale and not -log scale?

We improved the algorithm such that all four regions of RRHO plot are meaningful

list of result

hypermat

Matrix of -log(pvals) of the test for the first i,j elements of the lists.

Caleb

plotFolder <- 'plot'
system(paste('mkdir -p', plotFolder))
list.length <- 100
list.names <- paste('Gene',1:list.length, sep='')
set.seed(15213)
gene.list1<- data.frame(list.names, sample(100)*sample(c(1,-1),100,replace=TRUE))
gene.list2<- data.frame(list.names, sample(100)*sample(c(1,-1),100,replace=TRUE))
# Enrichment alternative
RRHO.example <-  RRHO2(gene.list1, gene.list2, 
                      labels=c('x','y'), plots=TRUE, outputdir=plotFolder, BY=TRUE, log10.ind=TRUE)