Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
DEGsTableDEGsHelpfileDescriptionThis function displays an object of class UsageDEGs.table(object) Arguments
Author(s)Toma Tebaldi, Erik Dassi, Galena Kostoska See Also
Examplesdata(tRanslatomeSampleData) DEGs.table(limma.DEGs) 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(tRanslatome)
Loading required package: limma
Loading required package: sigPathway
Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq
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 object is masked from 'package:limma':
plotMA
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.
Loading required package: edgeR
Loading required package: RankProd
Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: org.Hs.eg.db
Loading required package: GOSemSim
Loading required package: Heatplus
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: plotrix
Attaching package: 'plotrix'
The following object is masked from 'package:gplots':
plotCI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/DEGs.table.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DEGs.table
> ### Title: DEGsTableDEGsHelpfile
> ### Aliases: DEGs.table
> ### Keywords: DEGs DEGs.table
>
> ### ** Examples
>
> data(tRanslatomeSampleData)
> DEGs.table(limma.DEGs)
log2 FC (transcriptome) avg(transcriptome, undifferentiated)
A1CF 0.3915064248 2.573998
A4GALT 0.0652366640 2.438735
A4GNT 0.0388945313 2.200903
AAAS 0.0617816011 2.727900
AACS -0.0986524724 2.889455
AADAC 0.3284625337 2.551787
AAGAB -0.0525644826 2.640649
AAMP -0.0252859406 2.921980
AANAT 0.0044834224 1.844837
AARS 0.0068959813 3.084010
AARSD1 -0.1479566970 2.650221
AASDHPPT -0.0391872979 2.846465
AASS 0.3875872626 2.128366
AATF -0.0662754003 2.938589
ABAT 0.6596665581 2.059007
ABCA1 0.2938922747 2.326692
ABCA12 -0.4327181617 2.489473
ABCA2 -0.0049784265 2.422644
ABCA3 0.0585690909 2.430029
ABCA4 0.0007595326 2.123770
ABCA5 0.1914864651 2.438437
ABCA6 0.2632772583 1.898055
ABCA7 -0.0211561710 2.492543
ABCA8 0.6567107004 1.867956
ABCB1 0.3369725883 2.302782
ABCB4 0.2545844379 2.088508
ABCB6 -0.1339815744 2.707307
ABCB7 -0.0081636822 2.778817
ABCB8 0.0388645833 2.383394
ABCB9 0.0446595666 2.419282
ABCC1 0.0243176863 2.781705
ABCC10 -0.0717963881 2.648617
ABCC2 0.0384287860 2.754181
ABCC3 0.0665393126 2.766232
ABCC4 -0.0077012027 2.501523
ABCC5 -0.0577439099 2.630406
ABCC6 0.2401502497 2.262972
ABCC8 0.0522469855 2.271947
ABCC9 0.0143874616 2.143475
ABCD1 0.0800025003 2.365010
ABCD2 0.5111347452 1.715260
ABCD3 0.0270775871 3.137320
ABCD4 0.0233932651 2.479543
ABCE1 -0.1839123361 2.894500
ABCF1 -0.0412305075 2.993224
ABCF2 -0.0695853461 2.704634
ABCF3 -0.0089987331 2.693385
ABCG1 0.0645470846 2.010657
ABCG2 -0.1284238245 2.200485
ABCG4 0.0814558436 2.504833
ABCG5 0.1255390729 1.997825
ABHD10 0.0532716650 2.770018
ABHD11 0.0331234726 2.858576
ABHD2 0.1029507816 2.639032
ABHD3 -0.1205475238 2.370818
ABHD4 -0.0116138104 2.964753
ABHD5 -0.2017615382 2.446800
ABHD6 0.1625289421 2.381618
ABHD8 0.0119556275 2.468079
ABI1 -0.0008195858 2.569492
ABI2 -0.0294806509 2.650864
ABL1 -0.0326964924 2.727468
ABL2 0.0057686514 2.348320
ABLIM1 -0.0458181672 3.005136
ABLIM3 -0.1013723664 3.141802
ABO 0.0402511710 2.265895
ABP1 0.0862792179 2.238980
ABR -0.0330175474 2.371840
ABT1 -0.0064220256 2.811385
ABTB2 -0.1192567669 2.884221
ACAA1 0.1573003134 2.988120
ACAA2 0.0498742625 2.922962
ACACA -0.0843190250 2.783564
ACACB 0.1699310201 2.568497
ACAD10 0.1200105518 2.595586
ACAD8 0.2126499570 2.096094
ACADL 0.2042601414 2.795460
ACADM 0.1391648420 2.796768
ACADS 0.0523796351 2.738871
ACADSB 0.2033096181 1.828682
ACADVL 0.0171341499 3.227024
ACAP1 0.0903831879 2.357524
ACAP2 -0.0789226082 2.454962
ACAT1 0.1250247182 3.143441
ACAT2 -0.2573561315 2.977955
ACBD3 -0.0508822342 2.687682
ACBD4 0.0715041479 2.737846
ACCN1 0.1090466398 2.279522
ACCN2 0.0394204609 2.286108
ACCN3 0.0103976953 2.052852
ACCN4 0.0842808568 2.328246
ACD -0.2635797592 2.909381
ACE 0.0108951369 2.012875
ACE2 0.0572782810 2.154233
ACHE 0.0205068869 2.141281
ACIN1 0.0544627548 2.694924
ACLY -0.0655893556 3.051286
ACN9 0.0236835177 2.218725
ACO1 -0.0178769909 3.073200
ACO2 0.1157884916 2.525952
ACOT11 0.0986632838 2.549388
ACOT13 0.1004963018 3.175959
ACOT2 0.0234816200 2.807483
ACOT7 -0.1261441159 2.649350
ACOT8 0.1185092686 2.717514
ACOT9 -0.1217252208 2.985321
ACOX1 -0.0122611791 2.230919
ACOX2 0.0119256346 2.119373
ACOX3 -0.0321785917 2.501132
ACP1 0.0132038357 3.045451
ACP2 0.1168613808 2.703863
ACP5 0.0446320588 2.408964
ACP6 -0.0358767171 2.865751
ACPP 0.2001971252 1.794411
ACR 0.0715033033 2.219683
ACRV1 0.0502376221 2.117801
ACSBG1 0.0732724809 1.950946
ACSBG2 0.0448501206 2.415155
ACSF2 0.1249669335 2.455554
ACSL1 0.2313837043 3.125093
ACSL3 -0.1953353569 3.056869
ACSL4 0.3058445487 1.848668
ACSL5 0.0391766482 2.960313
ACSL6 0.0753484729 2.000580
ACSM1 0.0886640064 1.984366
ACSM2A 0.7928548777 2.249428
ACSM3 0.4068146861 2.172655
ACSM5 0.1429575817 2.218441
ACSS3 0.1374237074 2.620904
ACTA1 0.0625468989 1.996234
ACTA2 -0.1186830315 2.703798
ACTB -0.0095797069 3.475734
ACTC1 0.0433216845 2.604785
ACTG1 -0.1121269877 3.546669
ACTG2 0.0212821494 2.074655
ACTL6A -0.2567924108 2.609486
ACTL6B 0.0502484552 2.131320
ACTL7A 0.0696389988 2.343574
ACTL7B 0.0821234981 2.100988
ACTL8 -0.1550378960 3.222617
ACTN1 -0.4315800571 3.156445
ACTN2 0.0555686492 2.188636
ACTN4 -0.1221551845 3.147761
ACTR10 -0.0058571465 3.210641
ACTR1A -0.1517052663 2.908816
ACTR1B -0.0099232011 2.944889
ACTR2 -0.0324380031 2.944579
ACTR3 -0.1652555085 3.249154
ACTR3B -0.0397906584 2.219308
ACTR5 -0.0414301232 2.484830
ACTR6 -0.1479856252 2.399562
ACTR8 -0.0055931865 2.214754
ACVR1 0.0574990991 2.785118
ACVR1B 0.0829161690 2.397294
ACVR2A 0.0330671826 2.893484
ACVR2B -0.0617299872 2.365998
ACVRL1 0.0399780227 2.533420
ACYP1 -0.1554110108 2.530625
ACYP2 0.1940875654 2.628247
ADA -0.2051245188 2.760674
ADAM10 -0.1375388971 2.679565
ADAM11 0.0912791834 2.506189
ADAM12 -0.1309894630 2.391470
ADAM15 0.1388471292 2.425355
ADAM17 0.0409987188 2.490929
ADAM18 0.0213431735 1.819100
ADAM19 -0.0012868475 2.254196
ADAM20 0.0670314270 2.257509
ADAM21 0.0569583045 1.942918
ADAM22 0.0446039734 1.959237
ADAM23 0.1398963195 2.363001
ADAM28 0.0590795511 2.210653
ADAM29 0.0652892180 2.129920
ADAM30 0.1310738266 2.284279
ADAM7 0.0192426950 2.140118
ADAM8 0.0143145861 2.247562
ADAM9 -0.1796137992 3.068524
ADAMTS1 -0.1511661980 2.415576
ADAMTS12 0.0098132681 2.211528
ADAMTS13 0.0085288926 2.231909
ADAMTS2 -0.0418765774 2.379604
ADAMTS3 -0.1465531807 2.290514
ADAMTS5 -0.1407886815 2.216842
ADAMTS6 0.0579324686 1.987187
ADAMTS7 0.0392131705 2.344064
ADAMTS8 -0.0435577160 2.028873
ADAMTS9 -0.1070640156 2.270830
ADAMTSL2 0.0808637662 2.149592
ADAMTSL4 0.1365411074 2.368824
ADAP1 0.0825871070 2.564568
ADAP2 0.0432164564 2.254764
ADAR -0.0953378392 3.290218
ADARB1 0.0261205093 2.483311
ADARB2 0.0953087550 1.952534
ADAT1 -0.1110697686 2.555773
ADCK2 0.0125107265 2.537961
ADCK3 0.2627272795 2.706030
ADCK4 0.0645287657 1.978321
ADCY1 0.0635284117 2.262515
ADCY10 0.0451399984 1.956726
ADCY2 0.0265251717 2.096985
ADCY3 0.0126154024 2.369670
ADCY6 0.0114633586 2.639547
ADCY8 0.1984354976 2.264984
ADCY9 -0.0101786412 2.655891
ADCYAP1 0.0213369637 2.010398
ADCYAP1R1 -0.0113090069 1.946614
ADD1 -0.0267185119 2.874475
ADD2 0.0857094298 2.496454
ADD3 0.0390678919 2.841827
ADH1A 0.4814820779 1.989495
ADH1B 1.2725840564 1.966317
ADH6 0.5639613310 2.008952
ADH7 0.0257916974 1.885364
ADI1 -0.0212171655 3.229449
ADIPOR1 0.0607982267 2.815264
ADIPOR2 -0.0120916768 2.950041
ADK -0.0645230963 2.688231
ADM -0.0194895303 3.001683
ADM2 0.0712420803 2.702289
ADNP -0.0059682017 2.809829
ADNP2 -0.1252201487 2.736818
ADO -0.1144278752 2.723933
ADORA1 0.0531238036 2.275375
ADORA2A 0.0300378445 2.293416
ADORA2B 0.0372812376 2.310349
ADORA3 0.0083751297 2.233142
ADPGK -0.0481234520 2.982801
ADPRH 0.0593964625 1.996347
ADRA1A 0.1561998947 1.873223
ADRA1B 0.0697867761 1.845124
ADRA1D 0.0870174021 1.997273
ADRA2A 0.0433989053 1.810943
ADRB1 0.0576866778 1.791914
ADRB2 -0.3466237271 2.987628
ADRB3 0.0168309812 2.356604
ADRBK1 0.0451341840 2.594315
ADRBK2 0.0259650283 2.049491
ADRM1 -0.1696053467 3.097835
ADSS 0.0192416416 2.525475
AEBP1 -0.0023815807 2.474753
AEN -0.1326474666 2.915253
AES 0.0403123147 2.815565
AFF1 0.0795032531 2.529036
AFF2 0.0492832285 2.288808
AFF3 0.0295312449 1.995899
AFF4 0.0522276325 1.979608
AFG3L2 -0.0136511486 2.879642
AFM 0.3839149632 2.052539
AFP -0.2539844923 2.436212
AFTPH 0.0554987063 3.069559
AGA 0.1141942229 2.411605
AGAP1 0.1535127145 2.476193
AGAP2 0.1046473730 2.461493
AGAP4 0.0676410643 2.695349
AGAP7 0.0831577396 2.725692
AGBL2 0.1088985953 1.825424
AGBL5 -0.1940814450 2.698567
AGER 0.0627964460 2.148536
AGFG1 -0.0749241140 2.481027
AGFG2 0.0268772615 2.552559
AGGF1 -0.0182059807 2.475307
AGK 0.0026024564 2.842074
AGL 0.1460441066 2.678619
AGMAT 0.0469516660 2.015183
AGPAT1 0.0113584800 2.845666
AGPAT2 0.1456946647 2.684827
AGPAT3 0.1089472908 2.232720
AGPAT4 -0.0910850993 2.309972
AGPAT5 -0.1002118634 2.694805
AGPS -0.2302871029 2.528853
AGR2 -0.0377779397 2.491490
AGRN -0.0242418965 2.782634
AGRP 0.0079133321 2.417329
AGT 0.3724662559 3.114347
AGTPBP1 -0.0202009902 2.304707
AGTR1 -0.0240165981 2.036996
AGTR2 0.0473815418 1.993561
AGXT 0.3143449489 2.133313
AGXT2L1 0.3427859506 1.907407
AHCTF1 -0.0005986772 2.374889
AHCY -0.0950666794 2.975566
AHCYL1 -0.0004334916 3.183971
AHCYL2 0.0953966230 2.597883
AHDC1 -0.0184485903 2.327242
AHNAK 0.0435314477 2.852204
AHR 0.1574942656 2.816323
AHRR 0.0384914999 2.586756
AHSA1 -0.0872083566 3.068115
AHSG 0.2741533336 2.044474
AHSP 0.0526229494 2.313488
AICDA -0.0324216765 1.900438
AIDA -0.0438628439 2.127683
AIF1 0.0814361762 2.470941
AIFM1 0.1053871158 2.915453
AIM1 -0.0572842951 3.089181
AIM1L -0.1265955317 2.520428
AIM2 0.0256307241 2.183758
AIMP1 -0.1228761879 2.901515
AIMP2 -0.0844571098 3.049377
AIP 0.0168175802 2.835456
AIPL1 0.0519257046 2.215592
AIRE 0.0706568355 2.458900
AJAP1 0.0521086297 2.029956
AK1 0.0483618440 2.835246
AK2 0.0474691665 2.621034
AK4 0.0902868757 2.804975
AK5 0.0245235736 2.003936
AKAP1 0.0981978006 2.702957
AKAP10 -0.0001638202 2.385282
AKAP11 0.0282919992 2.401492
AKAP12 -0.1222996241 2.834063
AKAP13 0.0192676961 2.456195
AKAP17A 0.0418079052 2.415628
AKAP3 0.0656159508 2.021828
AKAP4 0.0220956102 2.086823
AKAP5 0.0317227288 1.879481
AKAP6 0.0840046119 1.965549
AKAP7 0.0694046738 2.152434
AKAP8 -0.1177612690 2.786536
AKAP8L 0.0252496368 2.455906
AKAP9 0.1669133569 2.348579
AKIP1 -0.0565648450 2.833687
AKIRIN1 0.1015104378 2.645826
AKIRIN2 0.1104072881 2.039656
AKR1A1 0.0313722142 3.263106
AKR1B1 -0.1948670477 2.951263
AKR1B10 -0.0480388626 3.734304
AKR1C1 0.0049572121 3.758719
AKR1C2 0.0486918957 3.537210
AKR1C3 0.0028747841 3.638825
AKR1C4 0.0681438368 2.152754
AKR7A2 -0.0159333033 3.004788
AKR7A3 0.2596408772 2.815053
AKT1 -0.0538039741 2.865415
AKT2 0.0101667018 2.112563
AKT3 -0.0279457591 2.381959
AKTIP 0.0316977366 2.538803
ALAD 0.1073867194 2.571501
ALAS1 -0.0591607782 2.932952
ALAS2 -0.0896451809 2.273225
ALB 0.5455255278 2.958616
ALCAM 0.0142103102 3.195283
ALDH18A1 -0.0219392085 2.732018
ALDH1A1 0.2906985736 3.162795
ALDH1A2 0.0671731583 2.229948
ALDH1A3 0.0687159660 1.861009
ALDH1B1 -0.0972530196 2.551422
ALDH1L1 0.2684052244 2.674717
ALDH2 0.2445270453 2.999032
ALDH3A1 -0.0377215085 3.219899
ALDH3A2 0.2194245475 3.036827
ALDH3B1 0.0999370113 2.802784
ALDH3B2 0.0967614380 1.947676
ALDH4A1 0.0808101181 2.747437
ALDH5A1 0.2272113646 2.127304
ALDH6A1 0.5161671035 2.347725
ALDH7A1 0.0608763390 2.682190
ALDH9A1 0.0432591637 3.152882
ALDOA 0.0197052463 3.515047
ALDOB 0.5164945384 2.206354
ALDOC 0.2204581551 2.756391
ALG12 0.1148300104 2.542170
ALG5 0.0285302660 2.945141
ALG6 0.0167748044
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and