estimate main effect

Description

estimates the main effects in an additive model.

Usage

estimateMainEffect(sgi, use.query = NULL)

Arguments

Details

The main effect is the single RNAi knockdown effect. When use.query is not specified, the main effect is estimated by minimizing the L1 distance from the non-interacting model to the double RNAi measurements. The implemented non-interacting model is the additive model (sum of single main effects). If the screen does not contain a lot of query genes with no or ery small main effect, it is recommended to estimate the template main effects only by using selected query genes. This can be obtained by specifying use.query. To estimate main effects in a multiplicative model define Transformation="log2" when creating the RNAinteract object (See createRNAinteractFromFiles), which is already the default.

Value

An object of class RNAinteract.

Author(s)

Bernd Fischer

References

~put references to the literature/web site here ~

See Also

RNAinteract-package

Examples

data("sgi")
sgi <- estimateMainEffect(sgi)
getMain(sgi)

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(RNAinteract)
Loading required package: abind
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAinteract/estimateMainEffect.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estimateMainEffect
> ### Title: estimate main effect
> ### Aliases: estimateMainEffect
> ### Keywords: manip
> 
> ### ** Examples
> 
> data("sgi")
> sgi <- estimateMainEffect(sgi)
> getMain(sgi)
, , area

                      1             2
SGI00013   2.347278e-02 -0.0124700491
SGI00017  -2.640730e-02 -0.1146857443
SGI00021   2.366594e-01  0.1490419305
SGI00109   6.811254e-02  0.0331411837
SGI00113  -3.806406e-02 -0.1674688543
SGI00117   2.644344e-01  0.1614570149
SGI00013   1.005479e-02 -0.0336347949
SGI00017  -1.099980e-02 -0.0956717997
SGI00021   2.437656e-01  0.1853955533
SGI00109   5.540585e-02  0.0279499083
SGI00113  -1.824184e-02 -0.2178506496
SGI00117   2.667386e-01  0.2612828635
SGI00025   1.501415e-02 -0.0392323207
SGI00029   2.843225e-02  0.0235897189
SGI00033  -4.594677e-01 -0.6159092110
SGI00121   3.544349e-02  0.0007183246
SGI00125   1.159710e-02 -0.0350692504
SGI00129  -5.014913e-01 -0.6334436365
SGI00025   9.022801e-03 -0.0233107662
SGI00029   2.283776e-02  0.0081186153
SGI00033  -5.683762e-01 -0.7723934267
SGI00121   2.685031e-02 -0.0131229885
SGI00125  -4.845714e-05 -0.0326148743
SGI00129  -6.389907e-01 -0.7498594912
SGI00002   6.825092e-03 -0.0247905766
SGI00006   3.959314e-02 -0.0017997507
SGI00010   2.519259e-02  0.0020214525
SGI00098   3.558704e-02  0.0159596545
SGI00102  -1.219216e-02 -0.1624677293
SGI00106   6.317700e-02  0.0320691520
SGI00002  -1.539012e-02 -0.0083105938
SGI00006   3.682916e-02  0.0010453653
SGI00010   1.423797e-02  0.0012242187
SGI00098   1.892241e-02  0.0044029190
SGI00102  -6.489198e-03 -0.1977769771
SGI00106   5.548890e-02  0.0381999193
SGI00014   2.890929e-02  0.0360653105
SGI00018  -3.947643e-02 -0.0272851385
SGI00022  -4.726965e-03 -0.0279165317
SGI00110   4.687472e-02  0.0718460386
SGI00114   1.372146e-02 -0.0108724141
SGI00118   4.007350e-02 -0.0051924788
SGI00014   1.877558e-02  0.0209275721
SGI00018  -3.908740e-02 -0.0427460806
SGI00022  -1.687426e-02 -0.0367870355
SGI00110   3.942740e-02  0.0518386413
SGI00114   7.261985e-04 -0.0151618357
SGI00118   3.967647e-02  0.0134359394
SGI00026   1.550476e-02 -0.0155642310
SGI00030  -7.654605e-02 -0.1201962277
SGI00034   1.619602e-02  0.0008452545
SGI00122   4.278570e-03 -0.0156313924
SGI00126  -1.218424e-01 -0.1890949376
SGI00130   4.201971e-02  0.0101303297
SGI00026   5.940185e-03 -0.0196755893
SGI00030  -9.185164e-02 -0.1249148529
SGI00034   7.843739e-03 -0.0064410169
SGI00122   7.717438e-03 -0.0178607426
SGI00126  -1.296009e-01 -0.1968792475
SGI00130   3.584392e-02 -0.0066607485
SGI00038  -1.436865e-01 -0.2240414026
Ctrl_Fluc -2.021367e-03  0.0083063545
SGI00046   3.731485e-02  0.0172227522
SGI00134  -1.105659e-01 -0.2014346588
Ctrl_th_2 -6.850433e-01 -0.8494048328
SGI00142   5.393652e-02  0.0373704569
SGI00038  -1.262345e-01 -0.1581542885
Ctrl_Fluc  2.021367e-03 -0.0083063545
SGI00046   2.428842e-02  0.0067163235
SGI00134  -8.448147e-02 -0.1433215765
Ctrl_th_2 -7.166912e-01 -0.8717884920
SGI00142   4.527176e-02  0.0364788135
SGI00062  -2.251141e-03 -0.0043317779
SGI00066   3.951330e-02  0.0227853571
SGI00070   2.338166e-02 -0.0141031591
SGI00158   4.614061e-02  0.0312213567
SGI00162   1.911416e-02 -0.0047463246
SGI00166   4.627693e-02  0.0250451778
SGI00062  -1.248774e-02 -0.0184731911
SGI00066   3.313668e-02  0.0170408416
SGI00070   1.619916e-02 -0.0522842908
SGI00158   4.218413e-02  0.0218403741
SGI00162   2.182306e-02 -0.0138743836
SGI00166   4.208972e-02  0.0143023473
SGI00074  -2.001180e-02 -0.0728032793
SGI00078   3.628353e-02 -0.0029890949
SGI00082   8.525028e-03 -0.0323506126
SGI00170   1.446783e-02 -0.0328721419
SGI00174   5.665328e-03 -0.0381264350
SGI00178   3.970855e-02  0.0099395446
SGI00074  -2.327486e-02 -0.0848404852
SGI00078   1.318120e-02 -0.0203199686
SGI00082  -7.615920e-06 -0.0355299400
SGI00170   6.860679e-03 -0.0551187874
SGI00174   1.932202e-03 -0.0434332218
SGI00178   2.496086e-02  0.0033066766

, , intensity

                     1            2
SGI00013  -0.007915142 -0.071663002
SGI00017  -0.168013008 -0.216251365
SGI00021   0.083516483 -0.023873228
SGI00109   0.085370816  0.010916080
SGI00113  -0.379338084 -0.369617291
SGI00117   0.177854974  0.086222333
SGI00013   0.021695656 -0.041155679
SGI00017  -0.138164449 -0.202626520
SGI00021   0.115470741 -0.004233892
SGI00109   0.133606979  0.024309053
SGI00113  -0.373777855 -0.390106221
SGI00117   0.239529685  0.120013846
SGI00025  -0.051354935 -0.091473023
SGI00029   0.038689151  0.031784108
SGI00033  -0.787778888 -0.618029642
SGI00121   0.005207487 -0.025412902
SGI00125  -0.088941254 -0.109957526
SGI00129  -0.668180144 -0.528969642
SGI00025  -0.003965033 -0.058735740
SGI00029   0.098346606  0.052001822
SGI00033  -0.803764179 -0.663464964
SGI00121   0.048481866 -0.013457431
SGI00125  -0.036177075 -0.078043583
SGI00129  -0.647866108 -0.565074555
SGI00002  -0.002450131 -0.052374005
SGI00006   0.010761522 -0.066894844
SGI00010  -0.005147140 -0.034134908
SGI00098   0.114198974  0.055027848
SGI00102  -0.242067273 -0.322939003
SGI00106   0.101368901  0.050796830
SGI00002   0.010705302 -0.025280034
SGI00006   0.045820625 -0.045748459
SGI00010   0.014188610 -0.012657713
SGI00098   0.156960967  0.057573144
SGI00102  -0.240119302 -0.390931223
SGI00106   0.148902126  0.091554283
SGI00014   0.144969587  0.142938766
SGI00018   0.096361044  0.025432373
SGI00022  -0.041027665 -0.079011185
SGI00110   0.221194027  0.218713920
SGI00114   0.034387960  0.014274737
SGI00118   0.031828903  0.011042374
SGI00014   0.168638229  0.193889930
SGI00018   0.137656964  0.019735797
SGI00022  -0.009779902 -0.062370690
SGI00110   0.267736928  0.257571117
SGI00114   0.088877604  0.045104802
SGI00118   0.070423217  0.028715091
SGI00026  -0.052399132 -0.080572264
SGI00030  -0.140211959 -0.172166776
SGI00034  -0.036721149 -0.086344542
SGI00122   0.021703864 -0.014152035
SGI00126  -0.260973101 -0.295129122
SGI00130   0.042328696 -0.013782540
SGI00026  -0.014740583 -0.068831844
SGI00030  -0.130261561 -0.165615342
SGI00034  -0.004815466 -0.081090643
SGI00122   0.086332255 -0.025537723
SGI00126  -0.244070048 -0.303715264
SGI00130   0.095745840 -0.013096466
SGI00038  -0.391233251 -0.402651774
Ctrl_Fluc -0.026799427  0.004830305
SGI00046  -0.087609678 -0.147257486
SGI00134  -0.244190889 -0.275215317
Ctrl_th_2 -0.911606328 -0.685711614
SGI00142   0.047592738 -0.019794581
SGI00038  -0.349499716 -0.325484705
Ctrl_Fluc  0.026799427 -0.004830305
SGI00046  -0.046721267 -0.132168512
SGI00134  -0.131897241 -0.210376999
Ctrl_th_2 -0.884263466 -0.761855384
SGI00142   0.086068187 -0.007576611
SGI00062   0.016945560 -0.013124926
SGI00066   0.060789168  0.014757559
SGI00070  -0.053762643 -0.100807610
SGI00158   0.033624025  0.018355054
SGI00162  -0.020825619 -0.052286892
SGI00166   0.033017202  0.018852616
SGI00062   0.021897322 -0.017574598
SGI00066   0.131651126  0.055842979
SGI00070  -0.023136182 -0.131914130
SGI00158   0.077456931  0.031260032
SGI00162   0.046267561 -0.032431406
SGI00166   0.085441459  0.031711282
SGI00074  -0.112865636 -0.158003160
SGI00078   0.041835993 -0.013515034
SGI00082  -0.087402282 -0.106770918
SGI00170  -0.059591143 -0.089065524
SGI00174  -0.093824588 -0.132580022
SGI00178   0.018159756  0.003327934
SGI00074  -0.079640648 -0.146372393
SGI00078   0.057134353 -0.016349853
SGI00082  -0.032297462 -0.103332238
SGI00170  -0.004871842 -0.084997683
SGI00174  -0.052482844 -0.096469958
SGI00178   0.059981393  0.015438797

, , nrCells

                     1             2
SGI00013  -0.018740956 -0.0735996948
SGI00017  -0.642135379 -0.7292503553
SGI00021  -0.658996311 -0.7296033354
SGI00109  -0.088490785 -0.1583096239
SGI00113  -0.769082065 -0.8051056845
SGI00117  -0.632444517 -0.7050549810
SGI00013   0.037808333 -0.0191924463
SGI00017  -0.608259973 -0.7198551961
SGI00021  -0.693147821 -0.7585857255
SGI00109   0.049159357 -0.0701138910
SGI00113  -0.796291866 -0.8586700005
SGI00117  -0.637224840 -0.7371886430
SGI00025  -0.066040836 -0.0896606060
SGI00029  -0.002682156 -0.0217564241
SGI00033  -1.375923299 -1.8798103125
SGI00121  -0.100063945 -0.1838426241
SGI00125  -0.034012276 -0.0992253464
SGI00129  -1.679427807 -1.9704127014
SGI00025   0.009538303  0.0301415054
SGI00029   0.087814632  0.0562748481
SGI00033  -1.676110075 -1.8790258446
SGI00121   0.004656202 -0.0648213545
SGI00125   0.045852639  0.0775198237
SGI00129  -1.605300118 -1.9532088361
SGI00002   0.002020049 -0.0290698952
SGI00006  -0.071189967 -0.1550745729
SGI00010   0.010101466 -0.0148101269
SGI00098   0.074084873 -0.0373297396
SGI00102  -0.474569521 -0.7278619470
SGI00106  -0.062716852 -0.0867649313
SGI00002   0.092207629  0.1152598523
SGI00006  -0.019809691 -0.0879925228
SGI00010   0.069538119  0.0894059240
SGI00098   0.106055432  0.0082851440
SGI00102  -0.507673281 -0.7552453747
SGI00106   0.066964943  0.0502891566
SGI00014   0.320197255  0.4515864512
SGI00018   0.010396937 -0.1427390205
SGI00022  -0.043367434 -0.0678354878
SGI00110   0.317048136  0.3711985890
SGI00114   0.083283854  0.0446464363
SGI00118  -0.012730862 -0.0215797457
SGI00014   0.399273180  0.6038244886
SGI00018   0.075014744 -0.1447033575
SGI00022   0.036497481  0.0083178020
SGI00110   0.386155191  0.5385372430
SGI00114   0.217333500  0.1985340159
SGI00118   0.064749388  0.0446896836
SGI00026   0.004407073  0.0132011183
SGI00030  -0.222175827 -0.2746952567
SGI00034  -0.021434475 -0.0584086791
SGI00122  -0.038436734 -0.0970898175
SGI00126  -0.239251142 -0.3560030213
SGI00130   0.004011324 -0.0582048306
SGI00026   0.102966677  0.1603552680
SGI00030  -0.159072097 -0.2460121828
SGI00034   0.037708681 -0.0193067070
SGI00122   0.087650291 -0.0245058601
SGI00126  -0.215366196 -0.3153667642
SGI00130   0.120868389 -0.0007345887
SGI00038  -0.609025014 -0.6452496741
Ctrl_Fluc -0.035162384  0.0078746620
SGI00046  -0.024443339 -0.1490499614
SGI00134  -0.559742697 -0.6663214096
Ctrl_th_2 -1.631504579 -1.4767913286
SGI00142  -0.008548041 -0.1823656640
SGI00038  -0.585909066 -0.5202781227
Ctrl_Fluc  0.035162384 -0.0078746620
SGI00046   0.080897937 -0.0296401759
SGI00134  -0.539374087 -0.5914798871
Ctrl_th_2 -1.832482011 -1.4738970492
SGI00142   0.096618474 -0.0943400137
SGI00062   0.054531116  0.1029480630
SGI00066  -0.057625433 -0.0824499717
SGI00070  -0.095350275 -0.1935863649
SGI00158  -0.042684531 -0.1035397937
SGI00162  -0.003293250 -0.0399873451
SGI00166  -0.073081258 -0.1082941351
SGI00062   0.117202883  0.1626641156
SGI00066   0.058543415  0.0574190371
SGI00070  -0.038296702 -0.1431112524
SGI00158   0.054537805  0.0382873127
SGI00162   0.114361352  0.0825238544
SGI00166   0.034357013  0.0024554726
SGI00074  -0.074032608 -0.1970957848
SGI00078  -0.049763565 -0.0947871230
SGI00082  -0.139055456 -0.1786098200
SGI00170  -0.211135053 -0.3261101202
SGI00174  -0.118680189 -0.1741702430
SGI00178  -0.067880169 -0.1127971074
SGI00074  -0.012078448 -0.1169821340
SGI00078   0.042307232  0.0073833569
SGI00082   0.002097301 -0.0944288704
SGI00170  -0.060155427 -0.3161446038
SGI00174   0.055682934 -0.0703627458
SGI00178   0.039895920 -0.0342216694

attr(,"axislabel")
                                        area 
"main effect (ratio), template (log2-scale)" 
                                   intensity 
"main effect (ratio), template (log2-scale)" 
                                     nrCells 
"main effect (ratio), template (log2-scale)" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>