| Previous changeset 13:3ef6de42310d (2019-10-03) |
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Commit message:
Uploaded |
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modified:
scoring function/KinatestScoring.xml |
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added:
scoring function/DATA/Fisher-Char.csv scoring function/DATA/Fisher-Table.csv |
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| diff -r 3ef6de42310d -r 6897a83b9096 scoring function/DATA/Fisher-Char.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scoring function/DATA/Fisher-Char.csv Mon Oct 07 14:48:16 2019 -0400 |
| b |
| b'@@ -0,0 +1,124 @@\n+"Normalization Score"\n+"0.144704867915654"\n+"Characterzation Table"\n+"threshold","Truepositives","Falsenegatives","Sensitivity","TrueNegatives","FalsePositives","One_Minus_Specificity","Accuracy","MCC","EER","Precision","FalsePositiveRate","F_One_Half","F_One","F_Two"\n+100,0,954,0,11793,0,0,92.5158860908449,NA,0.0748411390915509,NA,0,NA,NA,NA\n+99,0,954,0,11793,0,0,92.5158860908449,NA,0.0748411390915509,NA,0,NA,NA,NA\n+98,1,953,0.0010482180293501,11793,0,0,92.5237310739782,0.0311423230048369,0.0747626892602181,1,0,0.00626304801670146,0.00209424083769634,0.00130992926381975\n+97,11,943,0.0115303983228512,11793,0,0,92.6021809053111,0.103327941938382,0.0739781909468895,1,0,0.0661322645290581,0.0227979274611399,0.0143715704206951\n+96,24,930,0.0251572327044025,11793,0,0,92.7041656860438,0.152703439481177,0.0729583431395622,1,0,0.137142857142857,0.049079754601227,0.03125\n+95,37,917,0.0387840670859539,11793,0,0,92.8061504667765,0.1896994399291,0.071938495332235,1,0,0.201451905626134,0.0746720484359233,0.0480145341292499\n+94,49,905,0.0513626834381551,11793,0,0,92.9002902643759,0.21840789871475,0.0709970973562407,1,0,0.255652173913043,0.0977068793619143,0.0633893919793014\n+93,65,889,0.0681341719077568,11793,0,0,93.0258099945085,0.251710171649072,0.0697419000549149,1,0,0.321252059308072,0.127576054955839,0.0837413037876836\n+92,87,867,0.0911949685534591,11793,0,0,93.1983996234408,0.291461191104915,0.0680160037655919,1,0,0.400921658986175,0.167146974063401,0.111452728670254\n+91,101,853,0.105870020964361,11793,0,0,93.3082293873068,0.314211488490889,0.0669177061269318,1,0,0.446244477172312,0.191469194312796,0.128925197855502\n+90,114,840,0.119496855345912,11793,0,0,93.4102141680395,0.333992826795271,0.0658978583196046,1,0,0.485106382978723,0.213483146067416,0.145038167938931\n+89,125,829,0.131027253668763,11793,0,0,93.4965089825057,0.349887865156516,0.0650349101749431,1,0,0.515818431911967,0.231696014828545,0.158589190560771\n+88,144,810,0.150943396226415,11793,0,0,93.6455636620381,0.375822034999865,0.0635443633796187,1,0,0.564705882352941,0.262295081967213,0.181818181818182\n+87,164,790,0.171907756813417,11793,0,0,93.8024633247039,0.40139114523649,0.0619753667529615,1,0,0.611180124223602,0.293381037567084,0.206030150753769\n+86,173,781,0.181341719077568,11793,0,0,93.8730681729034,0.412405345125289,0.0612693182709657,1,0,0.630619684082625,0.307009760425909,0.216846327400351\n+85,187,767,0.19601677148847,11792,1,8.47960654625224e-05,93.9750529536362,0.427696010190806,0.0602494704636385,0.99468085106383,8.47960654625625e-05,0.65767878077374,0.327495621716287,0.233516483516484\n+84,198,756,0.207547169811321,11791,2,0.000169592130925156,94.053502784969,0.439099747221201,0.0594649721503099,0.99,0.000169592130925125,0.677309007981756,0.34315424610052,0.246513944223108\n+83,206,748,0.215932914046122,11791,2,0.000169592130925156,94.1162626500353,0.448126717902283,0.058837373499647,0.990384615384615,0.000169592130925125,0.692049272116461,0.354561101549053,0.25596421471173\n+82,221,733,0.231656184486373,11791,2,0.000169592130925156,94.2339373970346,0.464609640985605,0.057660626029654,0.991031390134529,0.000169592130925125,0.71830985915493,0.37553101104503,0.273582569943055\n+81,232,722,0.243186582809224,11790,3,0.000254388196387678,94.3123872283675,0.475197460606493,0.0568761277163254,0.987234042553191,0.000254388196387688,0.734952481520591,0.390243902439024,0.286349049617378\n+80,241,713,0.252620545073375,11790,3,0.000254388196387678,94.382992076567,0.484635721616722,0.0561700792343296,0.987704918032787,0.000254388196387688,0.749222797927461,0.402337228714524,0.29679802955665\n+79,250,704,0.262054507337526,11790,3,0.000254388196387678,94.4535969247666,0.493906981519595,0.0554640307523339,0.988142292490119,0.000254388196387688,0.762970498474059,0.414250207125104,0.307200786434013\n+78,259,695,0.271488469601677,11790,3,0.000254388196387678,94.5242017729662,0.503020490877378,0.0547579822703381,0.988549618320611,0.000254388196387688,0.77622377622377'..b'7,0.971698113207547,7932,3861,0.327397608750954,69.498705577783,0.350080954785325,0.30501294422217,0.193609022556391,0.327397608750954,0.276633840644584,0.322884012539185,0.538702928870293\n+0.9,931,23,0.975890985324948,7726,4067,0.344865598236242,67.9140189848592,0.340104369977249,0.320859810151408,0.186274509803922,0.344865598236242,0.266685763391578,0.312836021505376,0.528137054685727\n+0.8,934,20,0.979035639412998,7471,4322,0.366488594929195,65.937083235271,0.327437343758116,0.34062916764729,0.177701674277017,0.366488594929195,0.254982254982255,0.300805152979066,0.514770723104056\n+0.7,937,17,0.982180293501048,7209,4584,0.388705164080387,63.9052326037499,0.315159939373247,0.360947673962501,0.169715631226227,0.388705164080387,0.244031599965275,0.289420849420849,0.501767162900289\n+0.6,942,12,0.987421383647799,6897,4896,0.415161536504706,61.496822781831,0.302231669024383,0.38503177218169,0.161356628982528,0.415161536504706,0.23253517649963,0.277385159010601,0.487880671224363\n+0.5,944,10,0.989517819706499,6518,5275,0.447299245315017,5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| diff -r 3ef6de42310d -r 6897a83b9096 scoring function/DATA/Fisher-Table.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scoring function/DATA/Fisher-Table.csv Mon Oct 07 14:48:16 2019 -0400 |
| b |
| b'@@ -0,0 +1,88 @@\n+"Fisher Odds, only significant ones"\n+"A",0.45340758779271,0.655627376365787,0.71057968549539,1,1,1,0.661475174634559,1,3.03585759888931,1.51459592041551,1,1.34017319444569,1,1,1\n+"C",0,0.345209441541176,1,0.439204781206491,1,1,0.352417894571245,1,1,1,1,1,1,1,1\n+"D",0.594344633886148,1,1,1,1.66384233276824,1,1,1,0.684008070280575,0.662015100187512,0.106442479722756,1,1,0.46316688049323,0.549966497154065\n+"E",0.292663597118304,0.583743651981213,0.68785363302483,1,1.73531930467867,1,1,1,1,0.699013291179544,0.250510064922151,0.570840777287419,0.578425718913143,0.463622230477107,0.346051999957002\n+"F",0.299928538715751,0.310436870652965,0.546211326676489,0.466014130557673,1,0.392669958184368,0.597097123689267,1,0.541570812223002,1,1,1,1,1,0.507835584012799\n+"G",0.507623945499749,0.560540490034444,0.593549904924849,1,1,1,0.60671232074634,1,1.769935997282,0.659419442533899,1,1.45462269351531,1,1,1\n+"H",1,1,1,1,1,1,2.50389609103775,1,1,1,1,1,1.65900481512235,1,1\n+"I",0.403090488413341,0.307889860478955,0.547600827640001,0.345511377655714,0.60283010288607,1,3.05823613451316,1,0.515194263689111,1,1,0.633369164396449,1,1,0.396867085826232\n+"K",1,1,1,1,1,0.458383240093005,0.1287096104636,1,0.701009912366299,0.288631636584031,0.455674501541205,1,1.35612696686909,1.55717575281757,1.76729652730069\n+"L",0.339323960452766,0.427863792799034,0.58257580990574,0.683316669661594,0.47870380329021,0.70501086022765,1.27917299735765,1,0.525203302996324,0.629753643787753,1.4239312668024,1,0.604968180719687,1,0.348509548422124\n+"M",0.118175538397184,1,1,1,0.452657007403625,0.475486293211633,0.521956307038838,1,1,1,1,1,1,1,1\n+"N",0.41425029242714,1,1,1,1,1,1,1,0.67828428617815,1.41228957959503,1,1,1.44652110748644,1,1\n+"P",0.577837665797938,0.549821083126844,1,1,1,1,0.64579936166802,1,0.045523732528101,1,2.94555559055344,1,1,1,1\n+"Q",0.518539374013132,1,1,1,1,1,1,1,1.79387423793372,1.74580554895124,0.418050638841107,1.52022365407306,1,1.48950328454724,1.7938685808038\n+"R",0.35739315300058,0.234281870411409,1,0.473603694865266,0.253577019829549,0.0961602178021488,0.112752320370177,1,0.624891558617653,0.244684557040745,0.652593952330456,1,1.532364865378,1.55521688109415,1.65583207772368\n+"S",0.653865883150467,1,0.686753635902289,1,1,1,0.383691710807265,1,1.44652913016801,1.77550892638296,1,1.57586881623192,1.37373064173574,1,1\n+"T",0.598575452086606,1,1,1,1,1.38585946627246,1,1,1,1.42838786961092,1,1.68907801656503,1,1,0.558290684266478\n+"V",0.421531121464353,1,1,0.388912326878284,0.593625698898935,1,2.05383252772703,1,0.628206316369443,1.90581441973588,1.51079096904443,1,1,0.567107694598072,1\n+"W",0,0,1,0,0.0920717790410791,0.137486618706072,0.172105344749846,1,0.330200515876214,1,1,1,1,1,1\n+"Y",0.0927835451424165,0.392260258007587,0.389966359737425,1,0.23839662456134,0.19308426038567,0.602131676639123,1,1,1,1,1,1,1,0.519682643132409\n+"O",1.62273665634627,1.55349187509736,1.55945112858584,1.50054591916817,1.43582150640241,1,0.340533394157341,1,1,1,0.590441361088773,0.631741799315981,0.814063968142815,1,1.16231438005455\n+"Fisher Odds"\n+"A",0.45340758779271,0.655627376365787,0.71057968549539,0.922214710541857,1.12643960007807,1.22199406131933,0.661475174634559,0,3.03585759888931,1.51459592041551,1.15534418367196,1.34017319444569,0.994904775595518,1.16836795794878,0.709896564912449\n+"C",0,0.345209441541176,1.00146440899469,0.439204781206491,0.480018086191882,0.997249605052092,0.352417894571245,0,1.32075646428044,0.955276553953329,0.563859656272759,1.2716137634101,0.841492271928643,0.78142523113654,0.672574792091774\n+"D",0.594344633886148,0.952808800174973,0.686928651324403,1.18868652765991,1.66384233276824,1.15692657056969,0.934463963606677,0,0.684008070280575,0.662015100187512,0.106442479722756,0.734519203364876,0.936217223907015,0.46316688049323,0.549966497154065\n+"E",0.292663597118304,0.583743651981213,0.68785363302483,1.1265094031077,1.73531930467867,1.07249791413733,1.13107495559908,0,0.96623246499136,0.699013291179544,0.2505100649221'..b'01549889,0.699471727050123,0.00160835273447844,0.00161298023901304,0.000783638443219455\n+"S",0.0378848082387598,0.151520967936582,0.0462577758847013,0.506589726042649,0.945478825334824,0.0588094656544786,2.20463037061022e-07,1,0.00151179017445491,5.44800282256041e-07,0.892809804343377,0.000399922851093616,0.0216134737623335,0.585941732405277,0.362403393344275\n+"T",0.0429530960125628,0.220179475135355,0.0604752858304872,0.354689914552864,0.348818971928349,0.0173283547087478,0.455308843282568,1,0.0888605301414739,0.0113200863172584,0.0780931954142391,0.0001935505172109,0.454024862825873,0.447117162435407,0.0134768353999804\n+"V",0.000260052098753436,0.933077986578566,0.241653207636216,6.97888616605839e-06,0.00190900627191319,0.837645429810913,1.60188499584885e-11,1,0.00352595402803889,3.58147791102221e-08,0.00134677266689915,0.882119394980568,0.677766779256124,0.00484159539185242,0.648690261650646\n+"W",0.0109893142652081,0.00728689130487901,0.564487211549605,0.00224725138308303,0.000659390138837808,0.0113761204032523,0.00186088444334728,1,0.0387341965379344,0.224592288864352,0.759664030669416,0.830535551065552,0.332630936109219,0.246997577410753,0.422660069424239\n+"Y",3.31354806515718e-07,0.00208059028589647,0.00120485550858747,0.113719479355765,3.33162802184648e-06,1.83736657151628e-07,0.0227590008460977,1,0.315092743244122,0.448253815185915,0.326649921610956,0.237389850772931,0.754913153305204,0.584040860397283,0.0305578672473756\n+"O",2.25632728914017e-21,3.6949906958159e-16,8.37849471964426e-15,1.28899811025089e-10,3.32927971024485e-07,0.166809153340628,1.18301196567235e-09,1,0.628908004932332,0.89828595937171,2.23789272589542e-06,4.60940778059626e-07,0.0063179507946423,0.70023863375871,0.0097508690921711\n+"Fisher p.values adjusted"\n+"A",0.122795413691055,1,1,1,1,1,1,1,2.343505438935e-28,0.151932736091851,1,1,1,1,1\n+"C",0.0450700269303707,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+"D",1,1,1,1,0.0496251402511549,1,1,1,1,1,2.18574943514167e-11,1,1,0.203273958741314,1\n+"E",0.00144988434702009,1,1,1,0.000744001010330062,1,1,1,1,1,1.29432305369892e-08,0.750592195929664,0.549331971016308,0.0449007103952895,0.00169424013454612\n+"F",0.0614619353863486,0.113630122058304,1,0.359402483241389,1,0.211404778760815,1,1,0.880723393891192,1,1,1,1,1,1\n+"G",0.583976256767124,0.742455219718913,1,1,1,1,0.309563250083629,1,7.69659521897839e-06,1,1,0.938412089161546,1,1,1\n+"H",1,1,1,1,1,1,7.00044987883364e-07,1,1,1,1,1,1,1,1\n+"I",0.273140699310654,0.0112797955547782,1,0.00405401931171288,1,1,4.78348513257024e-27,1,0.128302414272547,1,1,1,1,1,0.207984619188537\n+"K",1,1,1,1,1,1,0.000172658632597143,1,1,9.47114852976229e-07,0.010684458976269,1,1,0.48017877905658,0.0100857887572787\n+"L",1.67589166481447e-05,0.00238563201824836,0.403223717820169,1,0.000549958124231666,1,1,1,0.00240531013034325,0.514612545179084,0.240854209082961,1,0.990940968985578,1,9.7443341282722e-05\n+"M",0.00575874540560851,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+"N",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+"P",1,1,1,1,1,1,1,1,2.51813533606161e-13,1,1.27762624149995e-22,1,1,1,1\n+"Q",1,1,1,1,1,1,1,1,0.0031851196429891,0.0127122716286365,0.0623357876626607,1,1,1,0.173026790739019\n+"R",1,0.989827443559247,1,1,0.06923453969436,0.000221353464359228,0.00279119425734096,1,1,9.86616899750547e-08,1,1,0.50663111136071,0.508088775289108,0.246846109614128\n+"S",1,1,1,1,1,1,6.94458566742219e-05,1,0.476213904953298,0.000171612088910653,1,0.125975698094489,1,1,1\n+"T",1,1,1,1,1,1,1,1,1,1,1,0.0609684129214335,1,1,1\n+"V",0.0819164111073322,1,1,0.00219834914230839,0.601336975652656,1,5.04593773692388e-09,1,1,1.128165541972e-05,0.424233390073231,1,1,1,1\n+"W",1,1,1,0.707884185671155,0.207707893733909,1,0.586178599654394,1,1,1,1,1,1,1,1\n+"Y",0.000104376764052451,0.655385940057387,0.379529485205053,1,0.00104946282688164,5.78770470027627e-05,1,1,1,1,1,1,1,1,1\n+"O",7.10743096079153e-19,1.16392206918201e-13,2.63922583668794e-12,4.0603440472903e-08,0.000104872310872713,1,3.7264876918679e-07,1,1,1,0.000704936208657058,0.000145196345088782,1,1,1\n' |
| b |
| diff -r 3ef6de42310d -r 6897a83b9096 scoring function/KinatestScoring.xml --- a/scoring function/KinatestScoring.xml Thu Oct 03 14:26:32 2019 -0400 +++ b/scoring function/KinatestScoring.xml Mon Oct 07 14:48:16 2019 -0400 |
| [ |
| @@ -5,8 +5,8 @@ </requirements> <command><![CDATA[ ln -s '$__tool_directory__/screener.csv' screener.csv && - ln -s '$FisherTable' Fisher-Char.csv && - ln -s '$CharacterizationTable' Fisher-Table.csv && + ln -s '$FisherTable' Fisher-Table.csv && + ln -s '$CharacterizationTable' Fisher-Char.csv && Rscript '$__tool_directory__/KinatestFisherScoring.R' $outGroup $Ms $Mfi $Mfo $Mth $Mtw $Mo $Dz $Po $Ptw $Pth $Pfo $Pfi $Ps ]]></command> <inputs> |