inst/script/example_data.R

In iteremoval: Iteration removal method for feature selection

library(GenomicRanges)
library(SummarizedExperiment)
library(utils)

table <- '"","G0Sample1","G0Sample2","G0Sample3","G0Sample4","G0Sample5","G0Sample6","G0Sample7","G0Sample8","G0Sample9","G0Sample10","G0Sample11","G0Sample12","G0Sample13","G0Sample14","G0Sample15","G0Sample16","G0Sample17","G0Sample18","G0Sample19","G0Sample20","G0Sample21","G0Sample22"
"Feature1",0.560957297,0.649451312,0.384542137,0.235775176,0.688333025,0.240656597,0.558012713,0.386356221,0.535499721,0.434947353,0.462284298,0.802797618,0.162729621,0.649809316,0.711916049,0.372861506,0.800992494,0.414665355,0.375352604,0.18109511,0.85765944,0.630343506
"Feature2",0.361587287,0.887827809,0.782349304,0.355777292,0.050471351,0.953107412,0.541557741,0.313227043,0.442985161,0.135835285,0.713548253,0.910703489,0.50459377,0.396529738,0.490863696,0.74890111,0.212800395,0.645253345,0.681124707,0.664892941,0.291308889,0.988175427
"Feature3",0.738803905,0.607882845,0.2136104,0.640840399,0.152624443,0.416911709,0.790060395,0.192455818,0.98142207,0.278218939,0.353405848,0.714363597,0.646625672,0.643822322,0.735743108,0.484121844,0.148957294,0.188359113,0.751039121,0.742880483,0.671800673,0.446573636
"Feature4",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
"Feature5",0.908661422,0.933915858,0.90025223,0.924197481,0.879866295,0.928445651,0.87924925,0.945101207,0.905190947,0.919447223,0.909805164,0.941621687,0.947107801,0.923165664,0.904622764,0.902075869,0.899644552,0.92542293,0.906952257,0.93439766,0.906877484,0.930706806
"Feature6",0.941232068,0.951233801,0.947097961,0.940196219,0.923813833,0.931757983,0.941366231,0.94820875,0.952839702,0.944178235,0.938907271,0.967103022,0.975774757,0.944244995,0.954822096,0.935492867,0.935475878,0.960398209,0.942526537,0.944010778,0.960313929,0.969887437
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"Feature24",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
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"Feature279",0.149025302,0.42097446,0.670587188,0.687421236,0.312423007,0.269258354,0.510549314,0.657162614,0.931632864,0.431021027,0.797523765,0.819655827,0.316223234,0.720474387,0.504899619,0.429512363,0.286807873,0.432501558,0.640911945,0.574681773,0.535213939,0.783629889
"Feature280",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
"Feature281",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
"Feature282",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
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"Feature284",0.561949014,0.503982546,0.63713174,0.35959353,0.961970155,0.710290364,0.805668289,0.679159267,0.881989934,0.317093622,0.255319484,0.143386105,0.330162346,0.563192831,0.661663031,0.387881173,0.422415737,0.363040122,0.69987537,0.380942581,0.479575106,0.768484448
"Feature285",0.436751038,0.133116762,0.471666881,0.472269393,0.886823203,0.355391079,0.388987246,0.873821852,0.898269808,0.673625318,0.178242008,0.173213705,0.038849187,0.901125706,0.193571914,0.690776252,0.812124861,0.769121743,0.537725999,0.374941156,0.196187057,0.322957288
"Feature286",0.796053498,0.57515847,0.32161679,0.578379501,0.50208964,0.428491708,0.644137926,0.363861576,0.791694547,0.256266031,0.929933414,0.706327588,0.462752812,0.503797874,0.660405886,0.836354654,0.627566159,0.293501282,0.926742585,0.40045531,0.901957449,0.692335831
"Feature287",0.727269849,0.615689397,0.931568308,0.854267185,0.760273526,0.596957535,0.457668264,0.582634378,0.525159686,0.830909431,0.863458499,0.608546346,0.649222633,0.893783345,0.585120699,0.758044627,0.481148565,0.622170886,0.540850301,0.639192801,0.862140732,0.783819941
"Feature288",0.756675296,0.611959848,0.731444573,0.890000874,0.777067939,0.620592244,0.488716721,0.61145894,0.543604923,0.890040295,0.764185855,0.632813003,0.68781571,0.929149806,0.602797898,0.603671037,0.505419006,0.658534144,0.572778631,0.670105794,0.885285165,0.803648289
"Feature289",0.277726802,0.213692855,0.151782235,0.303421729,0.418848244,0.863616935,0.425131786,0.21005095,0.9594664,0.88881666,0.959842771,0.567230883,0.286663914,0.235193465,0.620892102,0.500099342,0.929694623,0.680176966,0.958028737,0.767631164,0.383974488,0.417287222
"Feature290",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
"Feature291",0.824042658,0.879403073,0.190040208,0.314152648,0.31274136,0.237241674,0.602634077,0.749640757,0.965213786,0.879644028,0.874935505,0.803970094,0.397628824,0.797422197,0.781064546,0.510218018,0.184825349,0.456941632,0.390350661,0.967556589,0.834781665,0.415246745
"Feature292",0.783319699,0.824250552,0.183639899,0.301850947,0.313323571,0.264033355,0.516337492,0.714162486,0.953724589,0.875505323,0.89787652,0.805513255,0.39132045,0.763898125,0.762011838,0.501543712,0.187816821,0.460353078,0.385067573,0.962241118,0.854907063,0.399441718
"Feature293",0.788553406,0.833631871,0.18279456,0.297709957,0.318099352,0.265311586,0.517957672,0.71645483,0.952092552,0.871435355,0.90641497,0.785336271,0.385271092,0.75004427,0.794285082,0.596615451,0.18759569,0.448563579,0.380517723,0.984520409,0.839316715,0.395199983
"Feature294",0.758282195,0.741097674,0.182559046,0.291806882,0.432149208,0.277448201,0.521826084,0.595051259,0.962457544,0.83511546,0.87658891,0.765524625,0.39428261,0.721061449,0.79016812,0.576360318,0.196181286,0.430805721,0.513113248,0.959470645,0.922375716,0.503223893
"Feature295",0.748032728,0.813583838,0.594071871,0.572667606,0.838685018,0.677036762,0.626395841,0.653592109,0.967855288,0.635236879,0.883991968,0.745108784,0.725781372,0.774203967,0.620194814,0.845044613,0.591182391,0.638781342,0.89282787,0.664639239,0.651145957,0.623574137
"Feature296",0.7290036,0.816630037,0.589262374,0.672347573,0.811149363,0.670843114,0.62968916,0.652852436,0.974629667,0.627416191,0.830145484,0.725841724,0.70761261,0.702984144,0.620262921,0.856739749,0.602044528,0.642519143,0.824550378,0.65357429,0.648716798,0.628843316
"Feature297",0.701229572,0.788326151,0.711710006,0.787447343,0.820272471,0.742746707,0.733394536,0.804735463,0.95340657,0.732072936,0.719967726,0.73383226,0.766570915,0.701256826,0.722976943,0.865021258,0.715985299,0.729450832,0.709823016,0.74467326,0.74692817,0.727479446
"Feature298",0.633756851,0.655215196,0.650655142,0.735482717,0.805216812,0.689529765,0.675749789,0.775199298,0.982209123,0.689147698,0.64891449,0.680142547,0.747830357,0.651008164,0.662097749,0.83983685,0.675769017,0.808688646,0.661011452,0.714572529,0.694125901,0.692606979
"Feature299",0.619597435,0.641812676,0.86044152,0.636551113,0.631692436,0.702592395,0.679466563,0.977200326,0.693559651,0.692498705,0.712334474,0.687625439,0.729849931,0.697599367,0.650808216,0.72547588,0.645007936,0.68030818,0.679410177,0.698693422,0.684500745,0.71272759'

SWRG0 <- read.csv(text = table, row.names = 1)

table <- '"","G1Sample1","G1Sample2","G1Sample3","G1Sample4","G1Sample5","G1Sample6","G1Sample7","G1Sample8","G1Sample9","G1Sample10","G1Sample11","G1Sample12","G1Sample13","G1Sample14","G1Sample15","G1Sample16","G1Sample17","G1Sample18","G1Sample19","G1Sample20","G1Sample21","G1Sample22"
"Feature1",0.126787902,0.633813076,0.604370906,0.149027742,0.308895406,0.147172975,0.329180727,0.077198516,0.463454187,0.417420001,0.454023302,0.455793105,0.383039541,0.693562776,0.984304978,0.281237232,0.87817854,0.992663,0.655028754,0.104037389,0.52584697,0.372282385
"Feature2",0.745382411,0.439966714,0.001344662,0.080893604,0.347260691,0.376849839,0.018601287,0.520206559,0.982657262,0.82762331,0.237627294,0.613179228,0.840093712,0.527818185,0.220044191,0.620962704,0.983083264,0.986508052,0.25965785,0.907383913,0.617012653,0.440783193
"Feature3",0.767344347,0.01412433,0.576067041,0.991626081,0.473691233,0.533335893,0.019226613,0.410216558,0.548717292,0.730603139,0.278289348,0.875833233,0.099873765,0.560543944,0.994809,0.623637812,0.976939068,0.986349,0.162899042,0.980778774,0.232121041,0.696168187
"Feature4",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
"Feature5",0.920043309,0.911976021,0.982651574,0.940540516,0.906572932,0.911476703,0.918210302,0.887068771,0.885285654,0.893595144,0.919238456,0.930794877,0.964733684,0.925935071,0.991399,0.944846723,0.958976699,0.988411,0.961620204,0.927692971,0.953439266,0.962307984
"Feature6",0.971568526,0.953958308,0.990560303,0.956097666,0.961535129,0.941744244,0.952882594,0.949388199,0.934560483,0.945186782,0.955965747,0.969429667,0.975077193,0.96541739,0.987413991,0.96130561,0.964142413,0.981806,0.971540294,0.978180118,0.972679915,0.97836079
"Feature7",0.406985752,0.252086497,0.03214057,1.88e-05,0.013572703,0.001677,0.650621221,0.087806773,0.89439053,0.786167941,0.617918019,0.460504178,0.29592736,0.958929997,0.98594,0.720634032,0.979313848,0.981888,0.984049629,0.773358556,0.806829588,0.34114479
"Feature8",0.698737461,0.23885331,0.074783361,0.000117654,0.03586821,0.007287282,0.606859172,0.147081925,0.968684017,0.851235643,0.607727907,0.451281935,0.172971062,0.897269373,0.977817,0.705498794,0.980785144,0.981487,0.972335272,0.767206112,0.774065507,0.302179568
"Feature9",0.760329836,0.726990054,0.756596661,0.777957782,0.798856585,0.768784043,0.825011819,0.761094616,0.970797703,0.748229947,0.796192591,0.842261174,0.8326506,0.874544083,0.801501459,0.845760014,0.841202647,0.980598,0.839831435,0.841692958,0.87663461,0.822951217
"Feature10",0.568120165,0.671124166,0.980822966,0.356657953,0.59108454,0.492742681,0.579563064,0.233136853,0.883940944,0.367013689,0.596081634,0.271953551,0.736142299,0.594129436,0.984167,0.406630016,0.771940472,0.983136,0.732228828,0.767911559,0.488948337,0.651920216
"Feature11",0.42945365,0.884212314,0.988155676,0.988847517,0.51877426,0.390465858,0.366287857,0.898143388,0.886403453,0.908557569,0.596250929,0.391762279,0.631905437,0.916914375,0.99172,0.171784795,0.981674866,0.983863,0.726292885,0.99465089,0.871052697,0.18336279
"Feature12",0.551828752,0.86097856,0.992069997,0.983076556,0.626338035,0.50618745,0.934197774,0.709980882,0.984543881,0.941068067,0.535354875,0.50207928,0.970129361,0.9908871,0.988208,0.671709074,0.980784815,0.997933,0.639017919,0.980989252,0.990880043,0.703056617
"Feature13",0.981135323,0.515506661,0.987067256,0.989801516,0.686698254,0.597586053,0.971513812,0.62920164,0.980648189,0.809440357,0.762449027,0.598728034,0.969242165,0.973351228,0.991819,0.735856201,0.982123347,0.99789,0.474659095,0.993480148,0.991799054,0.762943356
"Feature14",0.722754549,0.927724521,0.998659152,0.791994525,0.952958412,0.824303063,0.88366788,0.479606709,0.995467538,0.75465405,0.649688616,0.915273285,0.894197707,0.960952767,0.981105,0.504738548,0.981612581,0.994287,0.421817716,0.982806889,0.945986642,0.446269574
"Feature15",0.614680806,0.918230745,0.981609668,0.197818458,0.773113216,0.762645466,0.706610098,0.610047863,0.980815676,0.65331212,0.607305887,0.973832272,0.636776289,0.944543871,0.979456,0.378954811,0.962234138,0.991657,0.432865015,0.987960732,0.785575111,0.173023928
"Feature16",0.230192193,0.934009093,0.978632248,0.275891215,0.860419867,0.829853526,0.548094432,0.626421548,0.974108091,0.58024217,0.618090524,0.973809219,0.711299673,0.894245674,0.985948,0.446145728,0.964867848,0.997936,0.501037236,0.977949709,0.814428271,0.214703661
"Feature17",0.66659661,0.923291196,0.820761111,0.034503438,0.04589582,0.192674443,0.15969209,0.187151848,0.239488956,0.207444392,0.345482158,0.226764623,0.583005812,0.344442773,0.524865529,0.449306266,0.582673203,0.999298,0.465582417,0.370347179,0.121442174,0.716697753
"Feature18",0.825594363,0.731716284,0.968385879,0.930893665,0.65075707,0.723085604,0.927333846,0.688609237,0.989491691,0.687146908,0.878536941,0.669870105,0.702125117,0.584138948,0.981339,0.906082878,0.656392885,0.9797,0.742182955,0.915890685,0.940836788,0.714012102
"Feature19",0.563224745,0.828655627,0.557011552,0.641164048,0.528285334,0.53112862,0.514456789,0.420511902,0.480864953,0.445630714,0.748969616,0.583237676,0.59439369,0.502223183,0.997181066,0.557107369,0.530749433,0.998732,0.671146589,0.538676476,0.557650016,0.576763213
"Feature20",0.249235977,0.849952031,0.799692307,0.806733558,0.915781592,0.438522958,0.255461129,0.236932107,0.61608101,0.459173775,0.946562128,0.204820956,0.838858288,0.920950313,0.984255168,0.363768065,0.528087337,0.983012796,0.287089814,0.537524475,0.75237579,0.771997246
"Feature21",0.936522741,0.862469529,0.408019141,0.817977073,0.765137851,0.474056716,0.236217324,0.304058174,0.809642426,0.585495835,0.863176335,0.22096528,0.872208586,0.898313448,0.986941412,0.40453845,0.504923829,0.9844,0.303519399,0.251727412,0.838516291,0.875310019
"Feature22",0.836198531,0.364264958,0.976982853,0.974440594,0.980640427,0.962751078,0.869453335,0.629513812,0.799669977,0.159549726,0.438848984,0.631052162,0.41843132,0.90366125,0.552426804,0.216069343,0.865836961,0.994415,0.602380559,0.92003451,0.854927746,0.734760706
"Feature23",0.67005144,0.980732315,0.571585228,0.978540718,0.676687505,0.922098292,0.976767481,0.447802269,0.973975121,0.803638249,0.668121833,0.685231465,0.636974028,0.900994764,0.991344,0.564707591,0.978570847,0.990597,0.660182957,0.972331618,0.638495571,0.627284033
"Feature24",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
"Feature25",0.827299644,0.768105444,0.808122335,0.831328031,0.831688715,0.845062789,0.734655886,0.6434189,0.636623867,0.620337448,0.664527012,0.623071984,0.666844202,0.606085661,0.826678149,0.681493758,0.604768892,0.994006,0.719953182,0.871583256,0.68186105,0.669519223
"Feature26",0.487506176,0.575469509,0.606694197,0.529812245,0.964452627,0.46490974,0.809465562,0.460070642,0.461815062,0.464540096,0.846194542,0.52004508,0.903170831,0.47972907,0.97321753,0.874345824,0.602495092,0.522299306,0.596054386,0.529693321,0.767866174,0.552773388
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SWRG1 <- read.csv(text = table, row.names = 1)

coordinates <- as(sprintf("%s:%s-%s", "chrN", 1:299, 2:300), "GRanges")

se1 <- SummarizedExperiment(assays=SimpleList(prob=as.matrix(SWRG1)),
                            rowRanges=coordinates,
                            colData=data.frame(Group=rep(1,22),
                                               row.names=colnames(SWRG1)))

se0 <- SummarizedExperiment(assays=SimpleList(prob=as.matrix(SWRG0)),
                            rowRanges=coordinates,
                            colData=data.frame(Group=rep(0,22),
                                               row.names=colnames(SWRG0)))

SummarizedData <- cbind(se1,se0)


save(SWRG1, file="data/SWRG1.rda")
save(SWRG0, file="data/SWRG0.rda")
save(SummarizedData, file="data/SummarizedData.rda")

rm(coordinates, se0, se1, table)