Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
plot of density functions of integrative correlationsDescriptionGiven a mergeExpressionSet, this function calculates and plots the density function of the approximate integrative correlations, as well as densities for the "null distributions" obtained by randomly permuting sample IDs. UsageintcorDens(x,method,...) Arguments
DetailsHere we use the approximate method to calculate the integrative correlation. ValueThe value is null. Returns a plot. See Also
Examples
if(require(Biobase) & require(MASS)){
data(mergeData)
merged <-mergeExprs(sample1,sample2,sample3)
intcorDens(merged)
intcorDens(merged,cex.legend=1.5)
intcorDens(merged,lty=2)
}
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(MergeMaid)
Loading required package: survival
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MergeMaid/intcorDens.Rd_%03d_medium.png", width=480, height=480)
> ### Name: intcorDens
> ### Title: plot of density functions of integrative correlations
> ### Aliases: intcorDens
> ### Keywords: hplot
>
> ### ** Examples
>
> if(require(Biobase) & require(MASS)){
+ data(mergeData)
+ merged <-mergeExprs(sample1,sample2,sample3)
+
+ intcorDens(merged)
+
+ intcorDens(merged,cex.legend=1.5)
+
+ intcorDens(merged,lty=2)
+ }
$...
[1] 1.254274e-01 8.040850e-02 -3.004128e-01 -2.627175e-02 -1.788983e-01
[6] -1.773959e-01 8.493976e-02 -4.891709e-02 -2.130056e-01 9.036953e-02
[11] -2.348724e-01 1.035757e-01 4.198838e-02 2.415086e-01 1.942043e-01
[16] -1.821532e-01 1.255337e-01 3.903430e-02 4.262297e-01 1.153753e-01
[21] 3.878416e-01 5.205459e-01 -3.021934e-01 4.727313e-02 2.073953e-01
[26] 2.329407e-01 -1.293712e-01 -1.578151e-01 -1.693218e-01 2.042468e-01
[31] 7.936279e-02 -9.683500e-03 -2.090572e-01 8.824853e-02 9.042177e-02
[36] -2.633675e-01 8.110216e-02 4.036722e-02 -5.020199e-01 7.149724e-03
[41] 2.739672e-01 1.629750e-01 -4.209518e-01 -2.112709e-01 -1.191182e-01
[46] 3.840837e-01 -3.842629e-01 3.189615e-01 1.106443e-01 -3.229358e-01
[51] 2.723925e-02 -1.063898e-01 2.626590e-01 -4.200780e-03 -1.430957e-01
[56] 9.330615e-02 1.768396e-01 -5.028485e-01 2.061820e-02 6.146406e-02
[61] -1.236047e-01 -3.898469e-01 6.758751e-02 1.600406e-01 1.400402e-01
[66] -1.080099e-01 -8.455880e-02 7.731745e-02 -1.689273e-01 2.497622e-01
[71] -1.220816e-02 4.682462e-01 3.998662e-02 -3.832943e-01 -2.081043e-01
[76] 1.348913e-01 -9.837463e-02 -1.358426e-01 3.219307e-01 6.494636e-03
[81] -4.015358e-02 1.361885e-01 -1.903325e-01 9.537790e-02 -2.787092e-01
[86] 1.273860e-01 -6.805704e-02 -2.260241e-01 1.260632e-01 3.115566e-03
[91] -2.253007e-01 -2.443700e-01 -9.841431e-02 -2.885059e-01 2.456108e-01
[96] 4.933346e-01 4.530714e-02 1.288216e-01 1.270949e-01 -4.721978e-01
[101] -7.727028e-02 -1.901834e-01 -1.544219e-01 1.465735e-01 3.756187e-01
[106] 2.239570e-01 -8.225238e-02 7.585964e-02 2.583676e-01 4.429015e-02
[111] 2.753065e-01 -1.743813e-01 2.866515e-01 -6.314197e-02 1.945665e-01
[116] 1.595168e-01 -9.466869e-02 1.499896e-01 -3.523838e-01 -9.323887e-02
[121] -1.995837e-02 2.024299e-01 -7.414386e-02 -1.032870e-01 -9.322423e-03
[126] 1.105722e-01 2.642186e-02 -2.318107e-01 -3.492347e-01 -1.419264e-01
[131] -2.906887e-01 -6.953473e-02 1.667247e-01 -2.285936e-01 -1.281815e-01
[136] 2.206082e-01 5.289500e-02 1.797669e-01 1.357158e-01 -1.130910e-01
[141] -2.741109e-01 -3.769259e-01 -1.004025e-02 1.240208e-01 -8.815167e-02
[146] 1.770817e-01 1.764049e-01 1.108629e-01 -1.415387e-01 -2.987371e-01
[151] 3.882410e-01 -1.750512e-01 3.031193e-01 4.832479e-01 -1.105265e-01
[156] 1.684405e-01 2.206993e-01 2.361627e-01 -1.947575e-01 1.155347e-01
[161] 1.357413e-01 -1.142561e-01 2.092676e-01 1.007405e-01 -2.690357e-01
[166] -2.066327e-01 -1.843056e-01 -1.879371e-01 -7.021260e-02 -3.542664e-01
[171] -5.203192e-02 -5.593800e-02 1.131301e-01 -1.929016e-02 -6.591176e-02
[176] 2.664856e-01 2.052942e-02 -3.787891e-02 2.205970e-01 -1.234055e-01
[181] 5.360474e-01 -3.861521e-01 -1.629895e-01 -3.802089e-01 3.542470e-02
[186] 2.247221e-01 -8.385078e-02 4.770696e-02 4.456321e-02 2.425554e-02
[191] -1.069761e-01 2.090150e-01 -2.287913e-01 6.300354e-02 -1.610551e-01
[196] -1.019598e-01 1.184911e-01 2.831202e-01 -3.878353e-01 1.900698e-01
[201] 2.025195e-02 -5.217397e-02 -2.847496e-02 5.099539e-01 -3.576605e-02
[206] -4.290343e-01 9.711873e-03 5.519107e-02 9.571932e-04 3.593777e-01
[211] 1.938612e-01 2.201405e-01 3.397486e-01 -5.458220e-02 2.196041e-01
[216] 1.921933e-01 -5.133837e-02 -2.072376e-01 -1.822619e-01 2.453498e-01
[221] 4.657752e-01 5.806408e-01 -2.035556e-02 -2.772347e-01 -1.003895e-01
[226] -2.152184e-01 -3.771689e-01 -1.777568e-01 2.623540e-02 2.317211e-01
[231] 2.794390e-01 9.837157e-02 -9.956788e-02 1.960678e-01 -7.685843e-02
[236] -3.454448e-02 -3.090320e-01 -1.665850e-02 -3.237824e-01 7.097019e-02
[241] 1.252145e-01 -4.215724e-02 -4.782787e-02 -2.609078e-01 1.338046e-01
[246] 2.850003e-02 -1.219483e-01 -3.231990e-01 9.088166e-02 -3.073708e-01
[251] -5.483658e-02 -1.791836e-01 4.577158e-01 1.262120e-01 -1.146915e-01
[256] -1.425240e-01 1.770368e-01 -2.888798e-01 1.614920e-01 3.082312e-01
[261] -5.011638e-02 2.344341e-02 1.033200e-01 2.358788e-01 -2.831120e-02
[266] -3.750582e-02 5.370226e-02 1.280516e-01 1.447100e-01 -2.467036e-01
[271] 3.937289e-03 -1.165532e-01 1.450274e-01 3.432737e-02 9.548187e-02
[276] -7.884268e-02 -2.005657e-01 -1.238265e-02 -4.310839e-02 1.773631e-02
[281] 3.897699e-01 -2.156452e-01 1.249740e-01 -1.909266e-01 -5.701588e-02
[286] -9.839341e-04 2.698746e-01 -2.048334e-01 8.226559e-02 7.620654e-02
[291] 1.714879e-01 5.739126e-01 -1.337164e-01 2.533338e-01 2.449521e-01
[296] -3.741614e-01 3.060974e-02 1.800466e-01 3.480474e-01 2.241804e-02
[301] 2.043067e-01 6.804070e-02 1.580985e-01 2.766947e-01 -2.987252e-01
[306] -7.930854e-02 1.933328e-01 2.558182e-01 -1.279475e-02 -8.574456e-02
[311] 2.590776e-01 6.019253e-02 -1.521082e-01 -3.317919e-02 -1.538640e-02
[316] -1.702986e-01 -4.776292e-02 1.496584e-01 -8.512920e-02 2.146097e-01
[321] 2.331417e-01 1.438362e-01 -2.765907e-01 3.681105e-01 3.510664e-01
[326] -5.575157e-02 -1.456613e-01 -8.484126e-02 2.583050e-01 1.810033e-02
[331] -5.242607e-02 3.256317e-01 -2.619043e-01 1.384533e-02 2.845266e-01
[336] 5.884408e-02 1.793043e-01 1.822880e-01 -4.111088e-01 -7.717301e-03
[341] -2.183207e-01 3.235051e-02 8.381205e-02 -2.966043e-01 1.492933e-01
[346] 1.909098e-01 8.984208e-02 6.541997e-02 1.524373e-01 -1.279474e-01
[351] 4.022460e-01 -4.183279e-01 -3.245220e-02 1.117727e-01 -3.343580e-01
[356] 2.975389e-02 3.192415e-01 3.907461e-02 1.862430e-01 -2.386958e-02
[361] 2.002576e-01 4.333625e-03 -5.658450e-02 -2.846546e-02 7.382631e-02
[366] 1.983469e-01 2.339490e-02 3.555263e-01 -4.019656e-01 1.254915e-01
[371] -6.506680e-02 1.848104e-01 -2.280284e-01 -9.327407e-02 -2.963143e-01
[376] -2.356548e-01 -1.601590e-01 5.198674e-01 1.770073e-01 1.137528e-01
[381] 1.845288e-01 9.477145e-02 -6.599971e-02 2.634548e-01 -6.049497e-02
[386] 1.659845e-02 -1.045089e-02 -1.021657e-01 -6.295870e-02 -3.880569e-01
[391] -1.564214e-01 3.237149e-01 -1.831209e-01 9.158683e-02 2.674255e-01
[396] 2.752266e-01 8.220915e-02 4.116153e-02 -1.554983e-01 -2.146362e-01
[401] 2.121771e-01 1.470980e-01 -1.973277e-01 -9.983209e-02 -1.200570e-01
[406] 6.285809e-02 -3.802237e-02 2.612362e-01 1.496137e-01 -2.027528e-01
[411] 1.490101e-01 -4.766597e-02 1.299743e-01 -2.419335e-01 -1.496416e-01
[416] -1.548434e-01 2.537009e-01 5.059399e-01 1.392715e-01 1.495267e-01
[421] -1.151330e-01 -2.633968e-01 -1.874981e-01 1.851481e-01 1.114745e-01
[426] 2.317444e-01 -1.176247e-01 8.853562e-03 -4.935317e-01 2.640849e-01
[431] -1.865547e-01 1.103218e-01 -1.468045e-01 1.994078e-01 1.339233e-02
[436] -2.012971e-01 -2.552796e-01 -4.795954e-01 -2.607439e-02 -1.752887e-01
[441] -1.499272e-02 -6.959344e-02 -2.040184e-02 -4.399300e-01 1.174383e-01
[446] -2.759283e-01 -4.475909e-02 -2.587064e-01 1.052356e-03 -2.129799e-01
[451] 1.681018e-01 4.290030e-01 2.461505e-01 -4.978536e-02 3.016376e-01
[456] -2.115880e-01 -5.857512e-02 2.237380e-02 -2.654000e-02 8.569221e-02
[461] 6.248764e-02 -4.898418e-01 -1.762973e-01 -1.008542e-01 -1.261739e-01
[466] 1.374604e-02 2.059700e-01 8.318454e-02 5.533502e-02 1.566232e-01
[471] -1.617391e-02 1.207590e-01 5.661315e-01 -1.641445e-01 9.158937e-02
[476] 3.882453e-01 -1.049774e-01 1.660927e-01 2.010232e-01 -5.499890e-01
[481] 5.935908e-02 -1.465579e-01 5.951113e-02 8.803540e-02 3.643926e-01
[486] 2.039211e-01 2.635907e-01 1.822274e-01 3.495226e-01 4.702419e-02
[491] -1.950634e-01 -6.463166e-02 -5.643216e-01 -2.674547e-01 -1.447070e-01
[496] 2.772427e-01 8.746600e-02 -3.946825e-02 -2.597162e-01 -1.739953e-02
[501] -2.355043e-01 -3.796885e-02 3.093281e-02 1.699739e-01 6.220383e-02
[506] 2.666669e-01 -1.280915e-01 2.093053e-01 7.642146e-02 -4.136205e-01
[511] -1.891392e-01 -2.027456e-01 -4.668859e-01 -3.975590e-02 3.038942e-01
[516] -1.511305e-01 -2.745772e-01 -2.586111e-01 -3.783431e-02 1.725588e-01
[521] -1.652847e-02 2.231307e-01 1.453852e-02 6.150704e-02 1.299254e-01
[526] 3.644438e-02 3.263274e-01 1.495821e-01 -1.912197e-01 -2.552700e-02
[531] 1.397636e-01 1.291478e-01 7.491240e-02 -2.213530e-01 -1.059539e-01
[536] 2.697238e-01 2.019409e-01 1.152576e-01 3.760554e-01 -2.258222e-01
[541] -1.116097e-02 8.117951e-02 2.903506e-01 2.738233e-01 -9.486186e-02
[546] -1.130489e-01 -9.107421e-02 -5.737267e-01 -2.225507e-01 -1.442328e-02
[551] -2.519337e-01 1.840042e-01 3.160653e-01 -2.253719e-01 -4.730305e-02
[556] 4.212815e-01 -2.924892e-01 -7.660296e-02 3.146982e-02 -1.327139e-01
[561] -2.983728e-02 -1.828829e-01 -3.112773e-02 2.709029e-01 3.343134e-02
[566] 2.482614e-01 5.143163e-02 -1.194002e-01 2.900836e-02 -1.379038e-01
[571] 2.783923e-01 6.357564e-02 1.337961e-01 -2.587401e-01 6.245423e-02
[576] 2.548947e-02 -1.725689e-01 7.555172e-03 1.396418e-02 -7.654166e-02
[581] 1.248247e-01 -1.081515e-01 5.655676e-02 -2.875263e-03 -1.872973e-01
[586] -2.980753e-01 4.235106e-02 3.285233e-02 -1.616717e-01 5.655796e-01
[591] -2.126816e-01 -8.621393e-02 -1.870593e-01 9.889536e-02 -5.607388e-02
[596] 1.011009e-02 -1.180653e-02 1.041023e-02 -2.364458e-01 -2.365318e-01
[601] -2.366508e-01 7.652578e-02 -9.292742e-02 3.039766e-01 -1.834257e-01
[606] -2.415829e-01 -1.573504e-01 -1.967232e-01 2.616742e-01 2.053831e-01
[611] 3.767241e-02 2.251113e-01 -9.025507e-02 -7.962833e-02 -6.531383e-02
[616] 7.771579e-02 1.954483e-01 2.015114e-01 -9.632847e-02 1.545422e-01
[621] -5.044199e-01 2.277636e-01 1.350043e-01 -2.265669e-01 -1.671791e-01
[626] 2.151247e-01 -7.018451e-02 1.620449e-01 -3.913001e-01 -3.391712e-02
[631] 3.557169e-01 5.800217e-01 -2.774025e-01 -1.129387e-01 2.885870e-02
[636] 1.822628e-03 3.664914e-01 9.393002e-02 9.759985e-02 2.336852e-02
[641] -1.349143e-01 2.061150e-01 -2.949834e-02 -3.068340e-01 -1.137683e-01
[646] -2.643527e-01 8.906426e-02 1.806205e-01 -5.254131e-02 -6.346395e-02
[651] 2.660612e-01 -3.430158e-01 1.349834e-01 -1.062233e-01 5.596190e-02
[656] -2.110843e-01 2.194128e-01 1.774588e-01 -1.270757e-01 3.290016e-01
[661] 1.103948e-01 1.585547e-01 2.416225e-01 1.867823e-01 -1.486994e-03
[666] 5.067182e-01 -2.945955e-01 3.398174e-01 1.315449e-01 4.223770e-01
[671] 1.781768e-01 4.529985e-02 -2.843274e-01 -1.268515e-01 -8.973543e-02
[676] 1.025989e-01 -1.049856e-01 -8.364728e-02 5.547312e-02 -5.239051e-02
[681] -3.879927e-02 -1.388962e-02 3.970268e-01 -3.231943e-01 2.128948e-01
[686] -3.463617e-02 1.138987e-01 -2.485070e-01 -8.193585e-02 -1.054893e-01
[691] 1.644282e-01 -1.987666e-01 2.794372e-02 -2.717829e-01 2.770882e-01
[696] -4.308291e-02 -8.086488e-02 -3.016708e-01 1.159809e-01 -1.584033e-01
[701] -9.471177e-02 1.455797e-01 7.837575e-02 1.994899e-01 2.389791e-01
[706] -4.827349e-01 2.608298e-01 3.780354e-01 6.808879e-02 -4.131092e-02
[711] 2.346757e-01 1.541766e-01 -3.008642e-01 -3.786387e-01 1.217299e-01
[716] -8.896342e-02 -1.160125e-01 2.698553e-01 1.594909e-01 7.396629e-02
[721] 7.701722e-02 -3.039836e-01 7.848120e-02 -1.131337e-02 2.056923e-01
[726] 2.238769e-01 -6.065073e-01 1.425344e-01 5.433633e-02 -1.206415e-01
[731] 3.025402e-01 -2.773715e-01 1.599375e-01 -1.130005e-02 -3.926670e-02
[736] -6.781530e-02 -2.857754e-01 1.585635e-01 -2.251765e-01 7.959503e-02
[741] 2.144975e-01 -7.373647e-02 6.942397e-02 3.813161e-01 -2.844689e-02
[746] -4.191740e-01 2.792577e-02 -1.912225e-01 1.038798e-01 1.392345e-02
[751] -4.400860e-02 1.216152e-01 -4.012356e-02 -9.644153e-02 2.271674e-01
[756] 5.037519e-02 -8.352722e-02 -1.786862e-01 -1.385586e-01 4.983024e-02
[761] -5.293237e-02 -2.082651e-01 8.564214e-02 5.224558e-02 -6.841880e-02
[766] 6.177558e-02 1.543470e-01 -2.878225e-01 -3.269172e-01 1.398801e-01
[771] -3.387558e-02 -2.087453e-01 -9.578166e-02 1.444825e-01 2.446038e-01
[776] -4.885288e-02 -2.003701e-02 -1.328481e-02 2.483752e-01 4.088012e-01
[781] -2.965043e-01 1.631980e-01 4.409979e-01 3.068888e-01 4.645427e-02
[786] -1.653341e-01 -5.236161e-02 1.012077e-02 -7.395095e-03 -3.607790e-01
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[1656] -1.459974e-01 2.694990e-01 -5.681859e-02 -1.541133e-01 5.679031e-01
[1661] -6.779283e-02 5.444589e-02 -2.103613e-01 -3.032638e-01 3.246553e-01
[1666] 6.050898e-02 7.642841e-02 8.636777e-02 1.279885e-01 4.032515e-01
[1671] 1.054822e-01 -1.130529e-02 1.078611e-01 -1.780693e-01 -6.413318e-02
[1676] -2.125813e-01 2.131168e-01 -4.739848e-01 -2.733681e-01 1.610714e-01
[1681] 3.661205e-01 3.210475e-01 -5.536494e-02 -6.387926e-02 1.456517e-01
[1686] -3.005940e-01 -9.019422e-02 -3.652657e-01 -9.602757e-02 3.109336e-02
[1691] 2.243860e-01 2.267546e-01 6.756628e-02 2.372447e-02 1.106900e-01
[1696] 1.614440e-01 2.165909e-01 3.297527e-01 6.709500e-02 7.434581e-02
[1701] 2.959507e-01 -2.824857e-01 -1.588665e-01 -3.073607e-01 -2.350182e-02
[1706] 6.630985e-02 -1.406865e-01 -1.731782e-01 3.515144e-01 -9.458529e-02
[1711] -1.528782e-01 -2.365300e-01 1.319266e-01 -2.166752e-01 -3.149956e-01
[1716] 1.131547e-01 2.870800e-01 3.405805e-01 -2.046695e-01 9.235219e-02
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[1726] -2.630885e-02 -8.335359e-02 -1.589367e-01 -3.429349e-01 -1.799470e-01
[1731] -1.609434e-02 -8.365961e-02 9.624813e-02 -2.591232e-01 8.125220e-02
[1736] -1.772424e-01 3.309843e-01 2.907344e-02 -2.218078e-01 -2.820255e-01
[1741] 1.207999e-01 2.063489e-01 1.433614e-01 2.128738e-01 3.677014e-01
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[1751] 1.280390e-01 1.031983e-01 2.692215e-01 -1.364211e-01 5.469774e-02
[1756] 1.853003e-02 1.019660e-01 1.587223e-01 -6.019132e-02 -1.145591e-01
[1761] 1.780431e-01 3.050541e-02 -2.320606e-01 3.529875e-01 -8.436916e-02
[1766] -2.975220e-01 -3.293525e-01 6.620918e-02 2.335467e-02 -3.910089e-04
[1771] -3.593877e-02 1.435232e-01 -3.188238e-01 -2.371875e-01 -1.159973e-01
[1776] -5.044796e-
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and