Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Accessors for a "DEXUSResult".DescriptionThese generic functions return the slots of an RNA-Seq
analysis performed by DEXUS. The results of DEXUS are
stored as an instance of Arguments
ValueThe accessor functions return a the matrices or vectors contained in the corresponding slot of the "DEXUSResult". Author(s)Guenter Klambauer klambauer@bioinf.jku.at and Thomas Unterthiner unterthiner@bioinf.jku.at Examplesdata(dexus) result <- dexus(countsBottomly[1:20,1:10]) transcriptNames(result) sampleNames(result) inputData(result) normalizedData(result) sizeFactors(result) INIValues(result) INIThreshold(result) INICalls(result) pvals(result) responsibilities(result) posteriorProbs(result) logFC(result) conditionSizes(result) sizeParameters(result) means(result) dispersions(result) params(result) 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(dexus)
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
Attaching package: 'dexus'
The following object is masked from 'package:BiocGenerics':
sizeFactors
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dexus/accessors.Rd_%03d_medium.png", width=480, height=480)
> ### Name: accessors
> ### Title: Accessors for a "DEXUSResult".
> ### Aliases: accessors conditionSizes dispersions INICalls INIThreshold
> ### INIValues inputData logFC means normalizedData params posteriorProbs
> ### pvals responsibilities sampleNames sizeFactors sizeParameters
> ### transcriptNames
>
> ### ** Examples
>
> data(dexus)
> result <- dexus(countsBottomly[1:20,1:10])
Filtered out 10 % of the genes due to low counts
Unsupervised mode.
> transcriptNames(result)
[1] "ENSMUSG00000000001" "ENSMUSG00000000003" "ENSMUSG00000000028"
[4] "ENSMUSG00000000031" "ENSMUSG00000000037" "ENSMUSG00000000049"
[7] "ENSMUSG00000000056" "ENSMUSG00000000058" "ENSMUSG00000000078"
[10] "ENSMUSG00000000085" "ENSMUSG00000000088" "ENSMUSG00000000093"
[13] "ENSMUSG00000000094" "ENSMUSG00000000103" "ENSMUSG00000000120"
[16] "ENSMUSG00000000125" "ENSMUSG00000000126" "ENSMUSG00000000127"
[19] "ENSMUSG00000000131" "ENSMUSG00000000134"
> sampleNames(result)
[1] "D2_1_4" "D2_2_4" "D2_3_4" "D2_5_4" "B6_6_4" "B6_7_4" "B6_8_4" "B6_1_6"
[9] "B6_2_6" "B6_3_6"
> inputData(result)
D2_1_4 D2_2_4 D2_3_4 D2_5_4 B6_6_4 B6_7_4 B6_8_4 B6_1_6
ENSMUSG00000000001 290 440 292 358 453 557 311 354
ENSMUSG00000000003 0 0 0 0 0 0 0 0
ENSMUSG00000000028 17 15 17 10 20 16 10 10
ENSMUSG00000000031 0 0 1 0 1 0 0 1
ENSMUSG00000000037 12 5 4 6 2 12 5 14
ENSMUSG00000000049 0 2 0 0 0 3 1 1
ENSMUSG00000000056 263 303 221 236 323 275 285 131
ENSMUSG00000000058 116 184 122 157 132 327 164 203
ENSMUSG00000000078 300 388 304 407 357 508 358 429
ENSMUSG00000000085 747 928 608 700 899 742 710 494
ENSMUSG00000000088 521 611 465 453 481 533 387 371
ENSMUSG00000000093 26 28 24 19 40 40 32 11
ENSMUSG00000000094 0 0 0 0 5 4 2 1
ENSMUSG00000000103 0 0 0 0 0 0 0 0
ENSMUSG00000000120 53 23 20 13 155 38 18 12
ENSMUSG00000000125 15 30 25 28 51 33 28 18
ENSMUSG00000000126 159 187 270 139 40 154 198 92
ENSMUSG00000000127 137 187 163 163 191 189 144 176
ENSMUSG00000000131 1380 1664 1213 1196 1549 1383 1344 778
ENSMUSG00000000134 635 625 519 487 598 557 508 266
B6_2_6 B6_3_6
ENSMUSG00000000001 275 328
ENSMUSG00000000003 0 0
ENSMUSG00000000028 5 16
ENSMUSG00000000031 0 0
ENSMUSG00000000037 6 2
ENSMUSG00000000049 0 4
ENSMUSG00000000056 168 99
ENSMUSG00000000058 160 169
ENSMUSG00000000078 287 319
ENSMUSG00000000085 481 513
ENSMUSG00000000088 318 351
ENSMUSG00000000093 12 25
ENSMUSG00000000094 5 1
ENSMUSG00000000103 0 0
ENSMUSG00000000120 20 23
ENSMUSG00000000125 19 22
ENSMUSG00000000126 44 61
ENSMUSG00000000127 131 131
ENSMUSG00000000131 697 849
ENSMUSG00000000134 302 336
> normalizedData(result)
D2_1_4 D2_2_4 D2_3_4 D2_5_4 B6_6_4
ENSMUSG00000000001 245.22934 372.504540 288.4427464 347.259055 351.153353
ENSMUSG00000000003 0.00000 0.000000 0.0000000 0.000000 0.000000
ENSMUSG00000000028 14.37551 12.699018 16.7928996 9.699974 15.503459
ENSMUSG00000000031 0.00000 0.000000 0.9878176 0.000000 0.775173
ENSMUSG00000000037 10.14742 4.233006 3.9512705 5.819984 1.550346
ENSMUSG00000000049 0.00000 1.693202 0.0000000 0.000000 0.000000
ENSMUSG00000000056 222.39764 256.520172 218.3076950 228.919377 250.380867
ENSMUSG00000000058 98.09173 155.774626 120.5137502 152.289586 102.322831
ENSMUSG00000000078 253.68552 328.481276 300.2965579 394.788926 276.736748
ENSMUSG00000000085 631.67695 785.645940 600.5931158 678.998152 696.880494
ENSMUSG00000000088 440.56719 517.273350 459.3351955 439.408804 372.858195
ENSMUSG00000000093 21.98608 23.704834 23.7076230 18.429950 31.006919
ENSMUSG00000000094 0.00000 0.000000 0.0000000 0.000000 3.875865
ENSMUSG00000000103 0.00000 0.000000 0.0000000 0.000000 0.000000
ENSMUSG00000000120 44.81778 19.471828 19.7563525 12.609966 120.151809
ENSMUSG00000000125 12.68428 25.398037 24.6954406 27.159926 39.533821
ENSMUSG00000000126 134.45333 158.314430 266.7107587 134.829633 31.006919
ENSMUSG00000000127 115.84972 158.314430 161.0142728 158.109570 148.058036
ENSMUSG00000000131 1166.95339 1408.744443 1198.2227787 1160.116843 1200.742921
ENSMUSG00000000134 536.96769 529.125767 512.6773472 472.388714 463.553432
B6_7_4 B6_8_4 B6_1_6 B6_2_6 B6_3_6
ENSMUSG00000000001 428.688076 312.877219 450.325115 367.603165 399.473136
ENSMUSG00000000003 0.000000 0.000000 0.000000 0.000000 0.000000
ENSMUSG00000000028 12.314200 10.060361 12.721048 6.683694 19.486494
ENSMUSG00000000031 0.000000 0.000000 1.272105 0.000000 0.000000
ENSMUSG00000000037 9.235650 5.030180 17.809468 8.020433 2.435812
ENSMUSG00000000049 2.308912 1.006036 1.272105 0.000000 4.871624
ENSMUSG00000000056 211.650307 286.720281 166.645735 224.572115 120.572684
ENSMUSG00000000058 251.671456 164.989916 258.237284 213.878205 205.826097
ENSMUSG00000000078 390.975840 360.160914 545.732979 383.644030 388.511983
ENSMUSG00000000085 571.071010 714.285612 628.419793 642.971354 624.785727
ENSMUSG00000000088 410.216777 389.335960 471.950898 425.082932 427.484971
ENSMUSG00000000093 30.785499 32.193154 13.993153 16.040865 30.447648
ENSMUSG00000000094 3.078550 2.012072 1.272105 6.683694 1.217906
ENSMUSG00000000103 0.000000 0.000000 0.000000 0.000000 0.000000
ENSMUSG00000000120 29.246224 18.108649 15.265258 26.734776 28.011836
ENSMUSG00000000125 25.398037 28.169010 22.897887 25.398037 26.793930
ENSMUSG00000000126 118.524172 199.195142 117.033646 58.816506 74.292260
ENSMUSG00000000127 145.461484 144.869195 223.890453 175.112780 159.545673
ENSMUSG00000000131 1064.408635 1352.112482 989.697569 931.706930 1034.002110
ENSMUSG00000000134 428.688076 511.066325 338.379889 403.695112 409.216383
> sizeFactors(result)
D2_1_4 D2_2_4 D2_3_4 D2_5_4 B6_6_4 B6_7_4 B6_8_4 B6_1_6
1.1825665 1.1811937 1.0123326 1.0309306 1.2900347 1.2993130 0.9940001 0.7860987
B6_2_6 B6_3_6
0.7480893 0.8210815
> INIValues(result)
ENSMUSG00000000001 ENSMUSG00000000003 ENSMUSG00000000028 ENSMUSG00000000031
2.482635e-10 2.295369e-20 1.731188e-07 3.259325e-20
ENSMUSG00000000037 ENSMUSG00000000049 ENSMUSG00000000056 ENSMUSG00000000058
3.161950e-07 1.415431e-06 6.915697e-02 3.019162e-07
ENSMUSG00000000078 ENSMUSG00000000085 ENSMUSG00000000088 ENSMUSG00000000093
2.268861e-07 5.067585e-10 9.272129e-11 9.994922e-08
ENSMUSG00000000094 ENSMUSG00000000103 ENSMUSG00000000120 ENSMUSG00000000125
2.335065e-06 1.484538e-20 1.690764e-01 1.646830e-08
ENSMUSG00000000126 ENSMUSG00000000127 ENSMUSG00000000131 ENSMUSG00000000134
3.403163e-02 6.195852e-08 1.448881e-09 2.095572e-09
> INIThreshold(result)
[1] 0.1
> INICalls(result)
ENSMUSG00000000001 ENSMUSG00000000003 ENSMUSG00000000028 ENSMUSG00000000031
FALSE FALSE FALSE FALSE
ENSMUSG00000000037 ENSMUSG00000000049 ENSMUSG00000000056 ENSMUSG00000000058
FALSE FALSE FALSE FALSE
ENSMUSG00000000078 ENSMUSG00000000085 ENSMUSG00000000088 ENSMUSG00000000093
FALSE FALSE FALSE FALSE
ENSMUSG00000000094 ENSMUSG00000000103 ENSMUSG00000000120 ENSMUSG00000000125
FALSE FALSE TRUE FALSE
ENSMUSG00000000126 ENSMUSG00000000127 ENSMUSG00000000131 ENSMUSG00000000134
FALSE FALSE FALSE FALSE
> pvals(result)
ENSMUSG00000000001 ENSMUSG00000000003 ENSMUSG00000000028 ENSMUSG00000000031
NA NA NA NA
ENSMUSG00000000037 ENSMUSG00000000049 ENSMUSG00000000056 ENSMUSG00000000058
NA NA NA NA
ENSMUSG00000000078 ENSMUSG00000000085 ENSMUSG00000000088 ENSMUSG00000000093
NA NA NA NA
ENSMUSG00000000094 ENSMUSG00000000103 ENSMUSG00000000120 ENSMUSG00000000125
NA NA NA NA
ENSMUSG00000000126 ENSMUSG00000000127 ENSMUSG00000000131 ENSMUSG00000000134
NA NA NA NA
> responsibilities(result)
D2_1_4 D2_2_4 D2_3_4 D2_5_4 B6_6_4 B6_7_4 B6_8_4 B6_1_6
ENSMUSG00000000001 1 1 1 1 1 1 1 1
ENSMUSG00000000003 1 1 1 1 1 1 1 1
ENSMUSG00000000028 1 1 1 1 1 1 1 1
ENSMUSG00000000031 1 1 1 1 1 1 1 1
ENSMUSG00000000037 1 1 1 1 1 1 1 1
ENSMUSG00000000049 1 1 1 1 1 1 1 1
ENSMUSG00000000056 1 1 1 1 1 1 1 1
ENSMUSG00000000058 1 1 1 1 1 1 1 1
ENSMUSG00000000078 1 1 1 1 1 1 1 1
ENSMUSG00000000085 1 1 1 1 1 1 1 1
ENSMUSG00000000088 1 1 1 1 1 1 1 1
ENSMUSG00000000093 1 1 1 1 1 1 1 1
ENSMUSG00000000094 1 1 1 1 1 1 1 1
ENSMUSG00000000103 1 1 1 1 1 1 1 1
ENSMUSG00000000120 1 1 1 1 2 1 1 1
ENSMUSG00000000125 1 1 1 1 1 1 1 1
ENSMUSG00000000126 1 1 1 1 1 1 1 1
ENSMUSG00000000127 1 1 1 1 1 1 1 1
ENSMUSG00000000131 1 1 1 1 1 1 1 1
ENSMUSG00000000134 1 1 1 1 1 1 1 1
B6_2_6 B6_3_6
ENSMUSG00000000001 1 1
ENSMUSG00000000003 1 1
ENSMUSG00000000028 1 1
ENSMUSG00000000031 1 1
ENSMUSG00000000037 1 1
ENSMUSG00000000049 1 1
ENSMUSG00000000056 1 2
ENSMUSG00000000058 1 1
ENSMUSG00000000078 1 1
ENSMUSG00000000085 1 1
ENSMUSG00000000088 1 1
ENSMUSG00000000093 1 1
ENSMUSG00000000094 1 1
ENSMUSG00000000103 1 1
ENSMUSG00000000120 1 1
ENSMUSG00000000125 1 1
ENSMUSG00000000126 1 1
ENSMUSG00000000127 1 1
ENSMUSG00000000131 1 1
ENSMUSG00000000134 1 1
> posteriorProbs(result)
, , 1
[,1] [,2] [,3] [,4] [,5]
[1,] 1.000000e+00 9.999999e-01 1.000000e+00 9.999999e-01 9.999999e-01
[2,] 1.200594e-15 5.760054e-08 1.098079e-10 6.518380e-08 7.110595e-08
[,6] [,7] [,8] [,9] [,10]
[1,] 1.000000e+00 1.000000e+00 1.000000e+00 9.999999e-01 1.00000e+00
[2,] 1.820798e-10 5.160068e-09 3.076253e-12 6.688367e-08 8.98562e-09
, , 2
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] NA NA NA NA NA NA NA NA NA NA
[2,] NA NA NA NA NA NA NA NA NA NA
, , 3
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999951e-01 9.999955e-01 9.999956e-01 9.999972e-01 9.999952e-01
[2,] 4.862112e-06 4.500127e-06 4.409761e-06 2.818297e-06 4.784886e-06
[,6] [,7] [,8] [,9] [,10]
[1,] 9.999957e-01 9.999969e-01 9.999955e-01 9.999989e-01 9.999970e-01
[2,] 4.342566e-06 3.053571e-06 4.508385e-06 1.082907e-06 3.032112e-06
, , 4
[,1] [,2] [,3] [,4] [,5]
[1,] 0.9998532131 0.9998532131 0.9998532131 0.9998532131 0.9998532131
[2,] 0.0001467869 0.0001467869 0.0001467869 0.0001467869 0.0001467869
[,6] [,7] [,8] [,9] [,10]
[1,] 0.9998532131 0.9998532131 0.9998532131 0.9998532131 0.9998532131
[2,] 0.0001467869 0.0001467869 0.0001467869 0.0001467869 0.0001467869
, , 5
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999991e-01 9.999977e-01 9.999978e-01 9.999973e-01 9.999993e-01
[2,] 9.489890e-07 2.319242e-06 2.171431e-06 2.703770e-06 6.784553e-07
[,6] [,7] [,8] [,9] [,10]
[1,] 9.999986e-01 9.999974e-01 1.000000e+00 9.99998e-01 9.999988e-01
[2,] 1.372711e-06 2.617230e-06 4.305684e-09 2.00224e-06 1.199217e-06
, , 6
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999949e-01 9.999947e-01 9.999949e-01 9.999949e-01 9.999949e-01
[2,] 5.051944e-06 5.303153e-06 5.051944e-06 5.051944e-06 5.051944e-06
[,6] [,7] [,8] [,9] [,10]
[1,] 9.999957e-01 9.999943e-01 9.999943e-01 9.999949e-01 9.999994e-01
[2,] 4.260328e-06 5.654379e-06 5.660505e-06 5.051944e-06 5.649637e-07
, , 7
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.9990441437 9.999313e-01 0.998649082 0.999441518 0.9998930874 0.997591298
[2,] 0.0009558563 6.866124e-05 0.001350918 0.000558482 0.0001069126 0.002408702
[,7] [,8] [,9] [,10]
[1,] 9.999908e-01 0.8198889 0.9992024742 0.01029574
[2,] 9.229440e-06 0.1801111 0.0007975258 0.98970426
, , 8
[,1] [,2] [,3] [,4] [,5]
[1,] 1.000000e+00 9.999881e-01 9.999999e-01 9.999892e-01 1.000000e+00
[2,] 4.229969e-11 1.188215e-05 1.083723e-07 1.075942e-05 2.591623e-10
[,6] [,7] [,8] [,9] [,10]
[1,] 1.000000e+00 9.999891e-01 1.000000e+00 1.000000e+00 1.000000e+00
[2,] 3.575857e-15 1.087967e-05 1.830032e-16 3.377819e-09 2.865068e-08
, , 9
[,1] [,2] [,3] [,4] [,5]
[1,] 1.000000e+00 9.999999e-01 1.000000e+00 9.999923e-01 1.000000e+00
[2,] 9.517969e-17 7.430570e-08 2.638627e-10 7.740095e-06 3.616158e-13
[,6] [,7] [,8] [,9] [,10]
[1,] 9.999920e-01 9.999971e-01 1.000000e+00 9.999922e-01 9.999919e-01
[2,] 8.017971e-06 2.855518e-06 2.275488e-17 7.772279e-06 8.051219e-06
, , 10
[,1] [,2] [,3] [,4] [,5]
[1,] 1.00000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
[2,] 2.40256e-09 3.688149e-10 9.792749e-11 2.817616e-08 3.453333e-08
[,6] [,7] [,8] [,9] [,10]
[1,] 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
[2,] 1.385569e-12 2.907387e-08 1.824628e-09 5.604598e-09 1.320394e-09
, , 11
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999999e-01 1.000000e+00 1.000000e+00 9.999999e-01 1.000000e+00
[2,] 6.487863e-08 2.098375e-10 3.940024e-08 6.557902e-08 1.968709e-09
[,6] [,7] [,8] [,9] [,10]
[1,] 1.000000e+00 1.000000e+00 1.000000e+00 9.999999e-01 9.999999e-01
[2,] 3.893212e-08 1.022199e-08 2.010597e-08 6.152921e-08 6.380130e-08
, , 12
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999997e-01 9.999995e-01 9.999995e-01 9.999999e-01 9.999990e-01
[2,] 3.175683e-07 4.705748e-07 4.708434e-07 1.066480e-07 1.049816e-06
[,6] [,7] [,8] [,9] [,10]
[1,] 9.999990e-01 9.999989e-01 1.000000e+00 1.000000e+00 9.99999e-01
[2,] 1.044413e-06 1.058858e-06 1.528669e-08 4.081664e-08 1.03396e-06
, , 13
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999944e-01 9.999944e-01 9.999944e-01 9.999944e-01 9.999982e-01
[2,] 5.624345e-06 5.624345e-06 5.624345e-06 5.624345e-06 1.753086e-06
[,6] [,7] [,8] [,9] [,10]
[1,] 9.999968e-01 9.999945e-01 9.999936e-01 9.999999e-01 9.999936e-01
[2,] 3.197102e-06 5.498222e-06 6.376599e-06 8.106605e-08 6.387440e-06
, , 14
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] NA NA NA NA NA NA NA NA NA NA
[2,] NA NA NA NA NA NA NA NA NA NA
, , 15
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.94283944 0.9993158716 0.9992872915 0.9997104017 1.077027e-06 0.996735006
[2,] 0.05716056 0.0006841284 0.0007127085 0.0002895983 9.999989e-01 0.003264994
[,7] [,8] [,9] [,10]
[1,] 0.9994349004 0.9996092173 0.997871232 0.997358914
[2,] 0.0005650996 0.0003907827 0.002128768 0.002641086
, , 16
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999997e-01 9.999958e-01 9.999959e-01 9.999957e-01 9.999993e-01
[2,] 3.025094e-07 4.225151e-06 4.118539e-06 4.267903e-06 6.539753e-07
[,6] [,7] [,8] [,9] [,10]
[1,] 9.999958e-01 9.999959e-01 9.999964e-01 9.999958e-01 9.999957e-01
[2,] 4.225151e-06 4.149863e-06 3.640614e-06 4.225151e-06 4.285675e-06
, , 17
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 9.999776e-01 9.999979e-01 1.00000e+00 9.999784e-01 0.7772367 0.9998929056
[2,] 2.240794e-05 2.089544e-06 3.37773e-11 2.159043e-05 0.2227633 0.0001070944
[,7] [,8] [,9] [,10]
[1,] 1.000000e+00 0.9998761458 0.97157852 0.992817543
[2,] 3.385832e-08 0.0001238542 0.02842148 0.007182457
, , 18
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999999e-01 9.999964e-01 9.999967e-01 9.999964e-01 9.999967e-01
[2,] 6.091403e-08 3.579229e-06 3.337882e-06 3.592893e-06 3.328784e-06
[,6] [,7] [,8] [,9] [,10]
[1,] 9.999970e-01 9.999971e-01 1.000000e+00 9.999987e-01 9.999965e-01
[2,] 2.995536e-06 2.909596e-06 5.845531e-11 1.303634e-06 3.482735e-06
, , 19
[,1] [,2] [,3] [,4] [,5]
[1,] 9.999999e-01 1.000000e+00 9.999999e-01 9.999999e-01 9.999999e-01
[2,] 1.346777e-07 8.555754e-16 1.415403e-07 1.199452e-07 1.373655e-07
[,6] [,7] [,8] [,9] [,10]
[1,] 1.000000e+00 1.000000e+00 1.00000e+00 1.00000e+00 1.000000e+00
[2,] 3.911323e-10 3.240143e-12 1.65016e-14 1.76104e-19 1.199548e-11
, , 20
[,1] [,2] [,3] [,4] [,5]
[1,] 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
[2,] 4.251505e-15 2.796365e-14 1.030905e-12 9.194022e-10 2.724304e-09
[,6] [,7] [,8] [,9] [,10]
[1,] 1.000000e+00 1.000000e+00 1.000000e+00 9.999999e-01 9.999999e-01
[2,] 4.445371e-08 1.430965e-12 3.136586e-10 7.077107e-08 7.161860e-08
> logFC(result)
Condition_1 Condition_2
ENSMUSG00000000001 0 9.020723e-03
ENSMUSG00000000003 NA NA
ENSMUSG00000000028 0 4.629497e-02
ENSMUSG00000000031 0 2.220446e-16
ENSMUSG00000000037 0 -1.974049e-01
ENSMUSG00000000049 0 -3.030703e-01
ENSMUSG00000000056 0 -5.880336e-01
ENSMUSG00000000058 0 -8.969066e-02
ENSMUSG00000000078 0 6.574189e-02
ENSMUSG00000000085 0 4.900779e-02
ENSMUSG00000000088 0 -2.529036e-03
ENSMUSG00000000093 0 1.782012e-01
ENSMUSG00000000094 0 -5.099409e-01
ENSMUSG00000000103 NA NA
ENSMUSG00000000120 0 1.583354e+00
ENSMUSG00000000125 0 4.830189e-03
ENSMUSG00000000126 0 -1.315769e+00
ENSMUSG00000000127 0 -2.519534e-02
ENSMUSG00000000131 0 2.713591e-02
ENSMUSG00000000134 0 -1.098290e-01
> conditionSizes(result)
Condition_1 Condition_2
ENSMUSG00000000001 1.0000000 2.752146e-08
ENSMUSG00000000003 1.0000000 0.000000e+00
ENSMUSG00000000028 0.9999963 3.739472e-06
ENSMUSG00000000031 0.9998532 1.467869e-04
ENSMUSG00000000037 0.9999984 1.601759e-06
ENSMUSG00000000049 0.9999953 4.670305e-06
ENSMUSG00000000056 0.8823928 1.176072e-01
ENSMUSG00000000058 0.9999966 3.366195e-06
ENSMUSG00000000078 0.9999965 3.451165e-06
ENSMUSG00000000085 1.0000000 1.034037e-08
ENSMUSG00000000088 1.0000000 3.666270e-08
ENSMUSG00000000093 0.9999994 5.608785e-07
ENSMUSG00000000094 0.9999954 4.579089e-06
ENSMUSG00000000103 1.0000000 0.000000e+00
ENSMUSG00000000120 0.8932163 1.067837e-01
ENSMUSG00000000125 0.9999966 3.409453e-06
ENSMUSG00000000126 0.9741356 2.586444e-02
ENSMUSG00000000127 0.9999975 2.459126e-06
ENSMUSG00000000131 0.9999999 5.339351e-08
ENSMUSG00000000134 1.0000000 1.908032e-08
> sizeParameters(result)
Condition_1 Condition_2
ENSMUSG00000000001 13.000000 13.000000
ENSMUSG00000000003 NA NA
ENSMUSG00000000028 9.555591 13.000000
ENSMUSG00000000031 13.000000 13.000000
ENSMUSG00000000037 2.659927 13.000000
ENSMUSG00000000049 1.309680 13.000000
ENSMUSG00000000056 13.000000 13.000000
ENSMUSG00000000058 9.766596 13.000000
ENSMUSG00000000078 13.000000 13.000000
ENSMUSG00000000085 13.000000 13.000000
ENSMUSG00000000088 13.000000 13.000000
ENSMUSG00000000093 12.959143 13.000000
ENSMUSG00000000094 1.328216 13.000000
ENSMUSG00000000103 NA NA
ENSMUSG00000000120 8.266070 5.415575
ENSMUSG00000000125 13.000000 13.000000
ENSMUSG00000000126 3.828333 4.466903
ENSMUSG00000000127 13.000000 13.000000
ENSMUSG00000000131 13.000000 13.000000
ENSMUSG00000000134 13.000000 13.000000
> means(result)
Condition_1 Condition_2
ENSMUSG00000000001 356.3555741 359.5847025
ENSMUSG00000000003 0.0000000 0.0000000
ENSMUSG00000000028 13.0336638 13.6512467
ENSMUSG00000000031 0.6535095 0.6535095
ENSMUSG00000000037 6.8233590 5.6009924
ENSMUSG00000000049 1.3651896 1.0082308
ENSMUSG00000000056 230.7327836 128.1531803
ENSMUSG00000000058 172.3595983 157.5735402
ENSMUSG00000000078 362.3013924 386.9201514
ENSMUSG00000000085 657.5328141 690.5597277
ENSMUSG00000000088 435.3514272 434.2517985
ENSMUSG00000000093 24.2295697 28.9559479
ENSMUSG00000000094 2.0140228 1.2094434
ENSMUSG00000000103 0.0000000 0.0000000
ENSMUSG00000000120 23.6434716 115.1740992
ENSMUSG00000000125 25.8128397 25.9378227
ENSMUSG00000000126 131.8123402 35.3609414
ENSMUSG00000000127 159.0225711 155.0659935
ENSMUSG00000000131 1150.6708090 1182.3228204
ENSMUSG00000000134 460.5758741 412.6701603
> dispersions(result)
Condition_1 Condition_2
ENSMUSG00000000001 0.07692308 0.07692308
ENSMUSG00000000003 NA NA
ENSMUSG00000000028 0.10465078 0.07692308
ENSMUSG00000000031 0.07692308 0.07692308
ENSMUSG00000000037 0.37595023 0.07692308
ENSMUSG00000000049 0.76354539 0.07692308
ENSMUSG00000000056 0.07692308 0.07692308
ENSMUSG00000000058 0.10238982 0.07692308
ENSMUSG00000000078 0.07692308 0.07692308
ENSMUSG00000000085 0.07692308 0.07692308
ENSMUSG00000000088 0.07692308 0.07692308
ENSMUSG00000000093 0.07716560 0.07692308
ENSMUSG00000000094 0.75288985 0.07692308
ENSMUSG00000000103 NA NA
ENSMUSG00000000120 0.12097647 0.18465259
ENSMUSG00000000125 0.07692308 0.07692308
ENSMUSG00000000126 0.26121027 0.22386875
ENSMUSG00000000127 0.07692308 0.07692308
ENSMUSG00000000131 0.07692308 0.07692308
ENSMUSG00000000134 0.07692308 0.07692308
> params(result)
$nclasses
[1] 2
$alphaINIT
[1] 0.5 0.5
$G
[1] 1
$cyc
[1] 20
$labels
NULL
$normalization
[1] "RLE"
$kmeansIter
[1] 10
$ignoreIfAllCountsSmaller
[1] 1
$theta
[1] 2.5
$minMu
[1] 0.5
$rmax
[1] 13
$initialization
[1] "kmeans"
$mode
[1] "unsupervised"
$multiclassPhiPoolingFunction
NULL
$quiet
[1] FALSE
$resultObject
[1] "S4"
>
>
>
>
>
> dev.off()
null device
1
>
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and