RRHOComparison: Compares two RRHO maps to a third
In zhilongjia/RRHO: Inference on agreement between ordered lists

Description Usage Arguments Details Value Author(s) References See Also Examples

Comparing two RRHO maps where one of the lists is shared between the two maps as in {RRHO map 1: list1 vs list3} vs {RRHO map 2: list2 vs list3}.

  RRHOComparison(list1, list2, list3, 
    stepsize, plots = FALSE, 
    labels, outputdir = NULL,
    log10.ind)

`list1`	A data.frame from experiment 1 with two columns, column 1 is the ‘Gene Identifier’, column 2 is the signed ranking value (e.g. signed -log10 of p-value, or fold change).
`list2`	Same as `list1`.
`list3`	Same as `list1`.
`stepsize`	Integer indicating how many genes to increase by in each algorithm iteration.
`labels`	Character vector carrying the labels for the outputted plots.
`plots`	Logical. Should comparisons be plotted?
`outputdir`	Plot destination directory.
`log10.ind`	Logical. Should pvalues be reported and plotted in -log10 scale and not -log scale?

The difference in {overlap between list1 and list3} compared to the {overlap between list2 and list3}. This is useful for determining if there is a statistically significant difference between two RRHO maps. In other words, this is useful for determining if the overlap between list1 and list3 is statistically different between the overlap between list2 and list3.

RRHO Difference maps are produced by calculating for each pixel the normal approximation of difference in log odds ratio and standard error of overlap between the two RRHO maps. This Z score is then converted to a P-value and corrected for multiple comparisons across pixels [3].

The function will return a RRHO of the significance of overlap between list1 and list3 and list2 and list3. A third RRHO gives the significance of the difference between these two overlap maps.

Note that by default all pvalues are outputted in -log scale. This can be changed with the log10.ind argument.

A oject including:

`hypermat1`	Pvalues of comparing `list1` to `list3`.
`hypermat2`	Pvalues of comparing `list2` to `list3`.
`Pdiff`	The pvalue of the test for a difference in difference between lists 1-3 and 2-3.
`Pdiff.by`	Pvalues, corrected for the search over all of the list using Benjamini-Yekutieli.

Jason Stein and Jonathan Rosenblatt

[1] Plaisier, Seema B., Richard Taschereau, Justin A. Wong, and Thomas G. Graeber. "Rank-rank Hypergeometric Overlap: Identification of Statistically Significant Overlap between Gene-Expression Signatures." Nucleic Acids Research 38, no. 17 (September 1, 2010): e169-e169.

[2] Benjamini, Y., and D. Yekutieli. "The Control of the False Discovery Rate in Multiple Testing under Dependency." ANNALS OF STATISTICS 29, no. 4 (2001): 1165-88.

[3] Stein JL*, de la Torre-Ubieta L*, Tian Y, Parikshak NN, Hernandez IA, Marchetto MC, Baker DK, Lu D, Lowe JK, Wexler EM, Muotri AR, Gage FH, Kosik KS, Geschwind DH. "A quantitative framework to evaluate modeling of cortical development by neural stem cells." Manuscript in press at Neuron. (*) Authors contributed equally to this work.

RRHO

  size<- 500
  list1<- data.frame(GeneIdentifier=paste('gen',1:size, sep=''), 
  RankingVal=-log(runif(size)))
  list2<- data.frame(GeneIdentifier=paste('gen',1:size, sep=''), 
  RankingVal=-log(runif(size)))
  list3<- data.frame(GeneIdentifier=paste('gen',1:size, sep=''), 
  RankingVal=-log(runif(size)))
  (temp.dir<- tempdir())
  RRHOComparison(list1,list2,list3,
                  stepsize=10,
                  labels=c("list1","list2","list3"),
                  plots=TRUE,
                  outputdir=temp.dir,
                  log10.ind=FALSE)