Compares two RRHO maps to a third

Description

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}.

Usage

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

Arguments

Details

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.

Value

A oject including:

Author(s)

Jason Stein and Jonathan Rosenblatt

References

[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.

See Also

RRHO

Examples

  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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RRHO)
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RRHO/RRHOComparison.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RRHOComparison
> ### Title: Compares two RRHO maps to a third
> ### Aliases: RRHOComparison
> 
> ### ** Examples
> 
>   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())
[1] "/tmp/RtmpCQNF7k"
>   RRHOComparison(list1,list2,list3,
+                   stepsize=10,
+                   labels=c("list1","list2","list3"),
+                   plots=TRUE,
+                   outputdir=temp.dir,
+                   log10.ind=FALSE)
$hypermat1
            [,1]       [,2]       [,3]       [,4]       [,5]       [,6]
 [1,] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
 [2,] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
 [3,] 0.00000000 0.00000000 0.50835912 0.29226075 0.17382903 1.01120162
 [4,] 0.00000000 0.00000000 0.29226075 0.13805340 0.29586261 0.93852840
 [5,] 0.00000000 0.00000000 0.17382903 0.06681333 0.13760658 0.47444195
 [6,] 0.00000000 0.00000000 0.10471430 0.03240677 0.06284724 0.23289028
 [7,] 0.00000000 0.00000000 0.28582251 0.09104712 0.10393244 0.25377323
 [8,] 0.00000000 0.00000000 0.19048361 0.04929748 0.14648551 0.26977271
 [9,] 0.00000000 0.00000000 0.12591275 0.09922291 0.18935424 0.28227837
[10,] 0.00000000 0.00000000 0.26205649 0.16292485 0.23208026 0.29217348
[11,] 0.00000000 0.00000000 0.18297839 0.09976855 0.27452251 0.30004923
[12,] 0.00000000 0.00000000 0.12604348 0.15349106 0.31669131 0.30631749
[13,] 0.00000000 0.00000000 0.08550780 0.09622431 0.19771074 0.17856500
[14,] 0.00000000 0.00000000 0.05704349 0.05860147 0.11883511 0.09884021
[15,] 0.00000000 0.02533822 0.11789485 0.09034539 0.14187478 0.10382945
[16,] 0.00000000 0.36384622 1.27123596 0.75839881 0.74352730 0.49755649
[17,] 0.00000000 0.29629230 1.03796634 0.88928765 0.79448266 0.49556830
[18,] 0.00000000 0.23962255 0.83952100 1.02980922 0.84620953 0.49329127
[19,] 0.00000000 0.19230173 0.67171530 0.79581676 0.61449701 0.32266602
[20,] 0.00000000 0.87425712 1.40096407 1.34280228 0.95307112 0.48794053
[21,] 0.00000000 0.74908707 1.74688338 1.51734288 1.00877656 0.48488773
[22,] 0.00000000 0.63802954 1.47536461 1.70570669 1.06640868 0.48158978
[23,] 0.00000000 0.53981308 1.23506404 1.38569176 0.80156092 0.31867275
[24,] 0.00000000 0.45330668 1.02353528 1.10950852 0.58699446 0.20122079
[25,] 0.00000000 0.79654026 1.31185952 1.76464225 0.90527832 0.31404844
[26,] 0.00000000 0.68226862 1.09298785 1.44203053 0.67193851 0.19807301
[27,] 0.00000000 1.12642248 1.39751768 1.63428290 0.71728979 0.19582853
[28,] 0.00000000 0.98129966 1.16945739 1.84735886 1.08075978 0.30400501
[29,] 0.00000000 0.84880738 0.96675762 1.51535575 0.81527164 0.19001143
[30,] 0.00000000 0.72831386 0.78809325 1.22300038 0.59691372 0.11161552
[31,] 0.00000000 0.61924613 0.63219365 1.40533255 0.63881601 0.10868070
[32,] 0.00000000 0.52107672 0.49780205 1.12411707 0.45330128 0.05874434
[33,] 0.00000000 0.43331124 0.38363528 1.30210734 0.48665553 0.05620703
[34,] 0.00000000 0.35547614 0.28834476 1.02983121 0.78271378 0.09751168
[35,] 0.00000000 0.66100064 0.41403535 1.20381875 0.83864935 0.09298673
[36,] 0.00000000 0.55252288 0.58206407 1.40767668 0.89990957 0.08805202
[37,] 0.00000000 0.45486265 0.44603435 1.10868772 0.64655094 0.04335171
[38,] 0.00000000 0.36779325 0.33138643 0.84829845 0.44232844 0.07693446
[39,] 0.00000000 0.70988442 0.48044994 1.01483107 0.47562464 0.13128321
[40,] 0.00000000 0.58481922 0.35286385 0.75738956 0.51218503 0.12206556
[41,] 0.00000000 0.47141352 0.24785525 0.54027288 0.32596088 0.11207361
[42,] 0.00000000 0.36984866 0.16451978 0.36345880 0.18930066 0.04978259
[43,] 0.00000000 0.28035553 0.10149799 0.22623557 0.09721520 0.01806602
[44,] 0.14850001 0.62074431 0.16192351 0.28134371 0.09888174 0.03421031
[45,] 0.12556322 0.47752735 0.25760782 0.35247668 0.21767636 0.13868486
[46,] 0.10314076 0.34817126 0.41450721 0.44786897 0.46820411 0.24899307
[47,] 0.08121006 0.23429996 0.69216636 0.58395047 0.51057794 0.21699349
[48,] 0.05975000 0.66412222 1.28136246 0.80065078 0.56409538 0.17699015
[49,] 0.03874083 0.43055727 0.83062526 1.23929987 1.65695964 0.90588920
[50,] 0.01816397 0.20184892 0.38936113 0.58086349 0.77652954 0.97654436
            [,7]       [,8]       [,9]      [,10]      [,11]      [,12]
 [1,] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
 [2,] 0.00000000 0.00000000 0.00000000 0.11319772 0.08472524 0.06317839
 [3,] 0.72612287 0.52056558 0.37101665 0.59593536 0.44202628 0.32434143
 [4,] 0.61996200 0.40464826 0.53689093 0.67548479 0.47262679 0.32422638
 [5,] 0.26773735 0.14648551 0.18935424 0.23208026 0.13546598 0.07597212
 [6,] 0.10930081 0.04863997 0.05983863 0.06981083 0.03259680 0.01432259
 [7,] 0.11045097 0.04467566 0.04615130 0.04644930 0.04588445 0.01906584
 [8,] 0.10907064 0.04009815 0.03542441 0.06845197 0.05819734 0.02286489
 [9,] 0.21120740 0.08020937 0.06067630 0.09162176 0.06933428 0.02574684
[10,] 0.19779352 0.06845197 0.04580938 0.06208364 0.07928143 0.02780944
[11,] 0.18489829 0.11369081 0.06933428 0.07928143 0.08809875 0.02916563
[12,] 0.29476319 0.28274541 0.16763070 0.16319494 0.15798037 0.09383480
[13,] 0.16068195 0.23977729 0.12910540 0.11529831 0.10268731 0.09117801
[14,] 0.08191612 0.20317888 0.09887892 0.13376972 0.10863111 0.08804835
[15,] 0.07652105 0.27274610 0.12737280 0.23433717 0.17696614 0.13316539
[16,] 0.33866039 0.71693030 0.51754818 0.70535586 0.52347118 0.52521291
[17,] 0.31243841 0.85292571 0.58702032 0.96765909 0.90443318 1.07730557
[18,] 0.43263217 1.00035228 0.65981797 1.00646081 0.89568003 1.01761979
[19,] 0.26522526 0.65790220 0.39312142 0.61687061 0.68680692 0.75639765
[20,] 0.53442741 1.03323797 0.61377424 0.84888773 0.88022345 0.91078830
[21,] 0.49504158 0.91874931 0.68533076 0.88595396 0.87334394 0.86245553
[22,] 0.45809917 1.06840487 0.76108511 0.92386665 0.86693840 0.81689105
[23,] 0.28755828 0.72065131 0.63842293 0.96282366 0.86095230 0.97570678
[24,] 0.26349074 0.63492455 0.53108725 0.78331278 0.66601224 0.73264329
[25,] 0.35946725 0.75253122 0.59429982 0.81901070 0.66193244 0.69337973
[26,] 0.21919716 0.48604937 0.35656010 0.49769243 0.37384794 0.38021830
[27,] 0.19879707 0.42164343 0.28688270 0.38700096 0.26937542 0.26022700
[28,] 0.27548668 0.50992612 0.32684267 0.40840856 0.26666635 0.24124432
[29,] 0.16117258 0.31042600 0.26066540 0.31197302 0.18545001 0.22280398
[30,] 0.08719078 0.17480085 0.20438344 0.23269180 0.18237451 0.20487556
[31,] 0.07612670 0.14349758 0.15713235 0.16880438 0.12119833 0.12926484
[32,] 0.03654831 0.11609436 0.11807811 0.11855155 0.11786716 0.11627967
[33,] 0.03061636 0.09234303 0.08640075 0.12503209 0.11409711 0.10373500
[34,] 0.14107108 0.28406090 0.23649661 0.28692588 0.24014492 0.20112027
[35,] 0.19935845 0.35041617 0.26900557 0.42432943 0.45830260 0.36166377
[36,] 0.17476538 0.29237770 0.20515668 0.31585245 0.32461716 0.23510642
[37,] 0.15135581 0.23974507 0.15165018 0.22647656 0.31646306 0.30244011
[38,] 0.21420666 0.29876733 0.26531086 0.34651070 0.43525282 0.53099795
[39,] 0.29894992 0.37093639 0.30119528 0.36267606 0.42596043 0.66712321
[40,] 0.26105112 0.30264376 0.22330131 0.25521959 0.28631022 0.45054250
[41,] 0.22412085 0.24026216 0.15799384 0.16907373 0.17858480 0.28159905
[42,] 0.10464607 0.10572199 0.10516048 0.10341298 0.25978228 0.36765137
[43,] 0.03972789 0.03659744 0.03312642 0.02956476 0.08900422 0.21053466
[44,] 0.05973370 0.04608713 0.03530357 0.02680501 0.07621375 0.17455686
[45,] 0.17880117 0.11675017 0.07599276 0.04899981 0.11666586 0.23452241
[46,] 0.26745772 0.14807249 0.16017675 0.08888256 0.17931483 0.31856164
[47,] 0.20290849 0.08749000 0.08325480 0.03443516 0.07330725 0.13743759
[48,] 0.13676516 0.04035242 0.03128399 0.02397311 0.04820866 0.08716249
[49,] 1.19833146 0.32521094 0.19736180 0.29077614 0.40550284 0.54185293
[50,] 1.18110566 0.46703362 0.18129020 0.24087859 0.30933129 0.38662960
           [,13]      [,14]       [,15]      [,16]      [,17]      [,18]
 [1,] 0.00000000 0.00000000 0.000000000 1.19732826 1.13320373 1.07294454
 [2,] 0.04688107 0.03458304 0.025338218 0.11395174 0.08798874 0.06735723
 [3,] 0.23497765 0.16778729 0.117894851 0.20747448 0.14957723 0.10590442
 [4,] 0.41949263 0.29095190 0.196985132 0.46541186 0.33302881 0.23262135
 [5,] 0.19771074 0.11883511 0.068516019 0.16579341 0.10067966 0.05853219
 [6,] 0.04312398 0.02027031 0.008945034 0.10806943 0.05832771 0.06095807
 [7,] 0.04302680 0.01851137 0.007348102 0.07115548 0.03394303 0.03141586
 [8,] 0.04150445 0.01632397 0.005814533 0.04693647 0.01966949 0.01601732
 [9,] 0.07378741 0.02911487 0.010228643 0.05669298 0.02261847 0.03123477
[10,] 0.06694145 0.02412246 0.015768572 0.06559030 0.02489563 0.05250179
[11,] 0.06031051 0.01979271 0.022252893 0.07361552 0.02655971 0.07983365
[12,] 0.14609922 0.05281664 0.051239263 0.19016578 0.07683280 0.16922237
[13,] 0.12889975 0.04250321 0.037367394 0.13374224 0.04740114 0.10193908
[14,] 0.11348413 0.03399626 0.026997489 0.09281434 0.02855645 0.05940623
[15,] 0.15244934 0.04570898 0.033125187 0.09775149 0.02843484 0.05327044
[16,] 0.69174460 0.28776067 0.209292065 0.39971788 0.15389333 0.22050159
[17,] 1.25956332 0.75507536 0.555204589 0.85437592 0.38117950 0.47426888
[18,] 1.40524519 0.82447120 0.582987225 0.84754082 0.47426888 0.55149507
[19,] 1.03710651 0.55240545 0.357605368 0.52474653 0.25633199 0.29144509
[20,] 1.16762232 0.77592109 0.496860704 0.66689652 0.32542939 0.34619269
[21,] 1.06392146 0.66922062 0.521572006 0.83000540 0.40487767 0.40621006
[22,] 0.96859869 0.57454508 0.422006200 0.66039901 0.29131860 0.27780198
[23,] 1.09332631 0.63102522 0.443609828 0.65715604 0.27497089 0.24765087
[24,] 0.99826729 0.54113998 0.465404109 0.65389710 0.34287739 0.38318018
[25,] 0.90986765 0.59468407 0.487468250 0.81152602 0.42123914 0.44408516
[26,] 0.50697622 0.29240211 0.297204066 0.51064715 0.22820014 0.23130318
[27,] 0.34082485 0.17448674 0.168449421 0.39337695 0.15565334 0.14899257
[28,] 0.29966309 0.19724340 0.178030351 0.39045970 0.14409930 0.12907937
[29,] 0.35487177 0.30212051 0.256884773 0.63684429 0.24979463 0.21179946
[30,] 0.31134166 0.24831708 0.197104459 0.49712487 0.17005382 0.33048522
[31,] 0.19483795 0.20118155 0.147749756 0.37926120 0.11071944 0.21814930
[32,] 0.16559628 0.16027513 0.107770618 0.28157515 0.06839028 0.13620504
[33,] 0.13901419 0.12518822 0.076126181 0.20237839 0.06052885 0.11496614
[34,] 0.33061837 0.27888680 0.167853720 0.36382022 0.16480976 0.26120369
[35,] 0.52226956 0.41832094 0.333701990 0.61227270 0.38108257 0.52552376
[36,] 0.33797890 0.34302159 0.253413834 0.46623601 0.26122013 0.35538410
[37,] 0.39987761 0.37991911 0.360963064 0.60209730 0.43560690 0.54123496
[38,] 0.83048155 0.74241637 0.665049296 0.98020784 0.69474026 0.80027768
[39,] 1.24043392 1.05701675 0.901895831 1.23613907 0.84450214 0.92210959
[40,] 0.87516787 0.69569114 0.950914648 1.25069240 1.02689464 1.06549528
[41,] 0.57676032 0.41758838 0.576406009 0.76541884 0.76084865 0.75658864
[42,] 0.68926331 0.46535196 0.604480937 1.00367722 0.94297711 0.88732856
[43,] 0.41711848 0.36212248 0.454318362 0.76198267 0.67185183 0.59207195
[44,] 0.34004550 0.26795508 0.321459786 0.54608702 0.44193692 0.35529911
[45,] 0.41514806 0.29618975 0.327615198 0.53238626 0.39182593 0.28344211
[46,] 0.51404318 0.51493784 0.515373049 0.75905416 0.51508982 0.51445031
[47,] 0.23333329 0.36637902 0.333696426 0.49337259 0.45028913 0.41080242
[48,] 0.14478622 0.22464864 0.175930798 0.26211819 0.20670831 0.16137899
[49,] 0.69993614 0.87976832 1.081346123 1.30469785 0.94450594 0.67292881
[50,] 0.47276264 0.56773975 0.671598848 0.78441245 0.90629227 1.03739308
           [,19]      [,20]      [,21]      [,22]      [,23]      [,24]
 [1,] 1.01611107 0.96233467 0.91130319 0.86274996 0.81644540 0.77219039
 [2,] 0.05107846 0.15301109 0.12060657 0.09408817 0.07257744 0.05530080
 [3,] 0.07352314 0.13016663 0.09205586 0.06369080 0.04303059 0.02833519
 [4,] 0.15817436 0.36830642 0.26242010 0.32640390 0.23102317 0.15876188
 [5,] 0.03246542 0.08260060 0.09573675 0.10955813 0.06538619 0.07502416
 [6,] 0.03131991 0.06493577 0.06631806 0.12072769 0.06794784 0.06822247
 [7,] 0.01382674 0.02636970 0.04609374 0.12755052 0.06775371 0.06077458
 [8,] 0.01292542 0.02089938 0.03197533 0.08048266 0.03768159 0.03004058
 [9,] 0.04159620 0.05378364 0.06787231 0.13305815 0.06295717 0.04643952
[10,] 0.06050948 0.06877345 0.07725375 0.13315953 0.05940879 0.04002460
[11,] 0.08221964 0.08415240 0.13107593 0.19409097 0.19425942 0.13266066
[12,] 0.15909334 0.14918981 0.20215899 0.26626473 0.24902472 0.16366151
[13,] 0.08844475 0.11532759 0.14683495 0.18326591 0.15944397 0.09402166
[14,] 0.04693676 0.05806206 0.15317265 0.17721095 0.14409385 0.07876201
[15,] 0.03851135 0.04378788 0.11063137 0.12026898 0.08970073 0.06566992
[16,] 0.15973627 0.16177975 0.30501931 0.30516818 0.30484488 0.22642002
[17,] 0.34331858 0.32542939 0.52186524 0.49530070 0.46976217 0.34287739
[18,] 0.38505838 0.34619269 0.52151686 0.47175487 0.42577039 0.29314598
[19,] 0.18086744 0.15065274 0.23505928 0.19709123 0.16400488 0.09623080
[20,] 0.20716991 0.16295655 0.23687811 0.25161510 0.19951523 0.11265249
[21,] 0.23505928 0.23687811 0.31442450 0.31469392 0.23912280 0.13030739
[22,] 0.14362582 0.13655302 0.23888342 0.22636002 0.15864730 0.14920511
[23,] 0.11814134 0.10495730 0.17825788 0.15864730 0.10129549 0.08860218
[24,] 0.24965771 0.28096768 0.40493866 0.34835972 0.22684904 0.19083468
[25,] 0.27840626 0.29563575 0.40337290 0.32979645 0.20178878 0.15915867
[26,] 0.12576185 0.17543032 0.23697776 0.17800906 0.09435660 0.06662065
[27,] 0.10168893 0.13532247 0.17563092 0.12135933 0.05661645 0.05279068
[28,] 0.08108397 0.10238244 0.12687056 0.11226332 0.09879256 0.08639051
[29,] 0.17873219 0.20393305 0.23063020 0.19457192 0.28870001 0.24495834
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