ideal User’s Guide (original) (raw)
We can run ideal for demonstration purpose on published datasets that are available as SummarizedExperiment in an experiment Bioconductor packages.
This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. More details such as gene models and count quantifications can be found in the airway package vignette.
To run ideal on this dataset, the following commands are required. First, prepare the objects to be passed as parameters of ideal.
Then launch the app itself.
The annotation for this dataset can be built manually by exploiting the org.Hs.eg.db package.
or alternatively, can be handily created at runtime in the optional step.
Coming from edgeR/limma-voom
Let’s suppose you performed part of your analysis with edgeR or limma/voom and you want to continue inspecting your data interactively using ideal. You can use the functionality provided by the DEFormats package to convert the object with:
library(DEFormats)
library(edgeR)#> Loading required package: limma#>
#> Attaching package: 'limma'#> The following object is masked from 'package:DESeq2':
#>
#> plotMA#> The following object is masked from 'package:BiocGenerics':
#>
#> plotMA#>
#> Attaching package: 'edgeR'#> The following object is masked from 'package:DEFormats':
#>
#> DGEListlibrary(limma)
dge_airway <- as.DGEList(dds_airway) # this is your initial object
# your factors for the design:
dex <- colData(dds_airway)$dex
cell <- colData(dds_airway)$cell
redo_dds_airway <- as.DESeqDataSet(dge_airway)
# force the design to ~cell + dex
design(redo_dds_airway) <- ~ cell + group # TODO: this is due to the not 100% re-conversion via DEFormats
### with edgeR
y <- calcNormFactors(dge_airway)
design <- model.matrix(~ cell + dex)
y <- estimateDisp(y, design)
# If you performed quasi-likelihood F-tests
fit <- glmQLFit(y, design)
qlf <- glmQLFTest(fit) # contrast for dexamethasone treatment
topTags(qlf)#> Coefficient: dexuntrt
#> seqnames
#> ENSG00000109906 11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11
#> ENSG00000165995 10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10
#> ENSG00000250978 5,5,5,5,5,5,5
#> ENSG00000168309 3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3
#> ENSG00000152583 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4
#> ENSG00000120129 5,5,5,5
#> ENSG00000189221 X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X
#> ENSG00000146250 6,6,6,6,6
#> ENSG00000171819 1,1,1,1,1,1,1,1
#> ENSG00000157214 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
#> start
#> ENSG00000109906 113930315,113930447,113930459,113930979,113931229,113932093,113933933,113933933,113933933,113933933,113935134,113992540,114027059,114027059,114051488,114057674,114057674,114057674,114107929,114112889,114112889,114117512,114117920,114117920,114117920,114117920,114121048,114121048,114121048,114121048
#> ENSG00000165995 18429606,18429666,18429676,18429721,18429887,18430109,18439812,18439812,18439812,18470736,18549698,18550190,18629646,18629666,18689742,18690853,18690853,18787284,18787284,18789741,18795400,18803165,18803440,18803909,18807265,18807839,18816517,18823005,18825030,18827109,18828159,18828159,18828159,18828159
#> ENSG00000250978 66759637,66760863,66761082,66762701,66763734,66771243,66771243
#> ENSG00000168309 58549844,58551188,58551188,58551579,58552935,58552946,58555418,58555418,58556053,58563036,58563036,58572585,58574933,58574933,58594601,58612698,58612698,58613143
#> ENSG00000152583 88394487,88394500,88394570,88400582,88401524,88403576,88411425,88411912,88412770,88414734,88414734,88415521,88415521,88415528,88415569,88415592,88415685,88416133,88416133,88416133,88416165,88418283,88420673,88420673,88425974,88449278,88449707,88449707,88450197,88450197,88450197,88450197,88450197,88450197,88450197,88450197,88451697,88452130,88452130
#> ENSG00000120129 172195093,172196578,172197164,172197589
#> ENSG00000189221 43515467,43515548,43515550,43517110,43542761,43542761,43552538,43552538,43571119,43571119,43571119,43571952,43571952,43587420,43587420,43590488,43590488,43590941,43591946,43595474,43599928,43601197,43602951,43603041,43603356,43603356,43603614,43603614,43603614
#> ENSG00000146250 84222194,84222257,84231254,84233141,84233141
#> ENSG00000171819 11249398,11252327,11253637,11253684,11254518,11254583,11254911,11254911
#> ENSG00000157214 89796904,89841000,89841058,89841174,89841187,89841200,89841245,89841590,89843134,89844588,89845805,89845809,89854364,89854364,89854364,89856285,89856285,89856285,89859186,89861651,89861651,89861651,89861651,89866205,89866205,89866205,89867413
#> end
#> ENSG00000109906 113930604,113930604,113930604,113931016,113931306,113932283,113934368,113934466,113935290,113935290,113935290,113992636,114027156,114027156,114051664,114057760,114057760,114060486,114108062,114113059,114113059,114118087,114118018,114118066,114118087,114118087,114121198,114121279,114121374,114121398
#> ENSG00000165995 18429785,18429785,18429785,18429785,18430144,18430144,18439904,18439904,18440198,18471036,18550246,18550246,18629906,18629906,18690029,18690972,18690972,18787406,18787722,18789877,18795476,18803298,18803459,18803970,18807345,18807897,18816626,18823156,18825125,18827294,18828653,18830038,18830056,18830798
#> ENSG00000250978 66759788,66761155,66761155,66762766,66763881,66771305,66771420
#> ENSG00000168309 58552422,58552422,58553091,58552422,58553091,58553091,58555592,58555592,58556150,58563115,58563491,58572840,58574996,58574996,58594984,58613147,58613337,58613337
#> ENSG00000152583 88394955,88394955,88394955,88400730,88401672,88403712,88411545,88412030,88412842,88415750,88415750,88415750,88415750,88415750,88415750,88415750,88415750,88416279,88416279,88416295,88416279,88418391,88420737,88420737,88426075,88449385,88449766,88449771,88450244,88450253,88450393,88450524,88450556,88450609,88450655,88450656,88451783,88452201,88452213
#> ENSG00000120129 172196135,172196797,172197309,172198198
#> ENSG00000189221 43515662,43515662,43515662,43517217,43542855,43542855,43552675,43552675,43571223,43571223,43571223,43572043,43572043,43587561,43587561,43590629,43590637,43591100,43592042,43595527,43599985,43601294,43603152,43603152,43603418,43603418,43603905,43604409,43606068
#> ENSG00000146250 84222413,84222413,84231358,84235419,84235423
#> ENSG00000171819 11250012,11252427,11253831,11253831,11254716,11254716,11255235,11256038
#> ENSG00000157214 89797227,89841359,89841359,89841248,89841359,89841359,89841359,89841650,89843174,89845917,89845917,89845917,89854660,89854888,89854888,89856337,89856347,89856812,89859350,89861798,89861938,89866908,89866945,89866922,89866945,89866992,89867451
#> width
#> ENSG00000109906 290,158,146,38,78,191,436,534,1358,1358,157,97,98,98,177,87,87,2813,134,171,171,576,99,147,168,168,151,232,327,351
#> ENSG00000165995 180,120,110,65,258,36,93,93,387,301,549,57,261,241,288,120,120,123,439,137,77,134,20,62,81,59,110,152,96,186,495,1880,1898,2640
#> ENSG00000250978 152,293,74,66,148,63,178
#> ENSG00000168309 2579,1235,1904,844,157,146,175,175,98,80,456,256,64,64,384,450,640,195
#> ENSG00000152583 469,456,386,149,149,137,121,119,73,1017,1017,230,230,223,182,159,66,147,147,163,115,109,65,65,102,108,60,65,48,57,197,328,360,413,459,460,87,72,84
#> ENSG00000120129 1043,220,146,610
#> ENSG00000189221 196,115,113,108,95,95,138,138,105,105,105,92,92,142,142,142,150,160,97,54,58,98,202,112,63,63,292,796,2455
#> ENSG00000146250 220,157,105,2279,2283
#> ENSG00000171819 615,101,195,148,199,134,325,1128
#> ENSG00000157214 324,360,302,75,173,160,115,61,41,1330,113,109,297,525,525,53,63,528,165,148,288,5258,5295,718,741,788,39
#> strand
#> ENSG00000109906 +,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+
#> ENSG00000165995 +,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+
#> ENSG00000250978 -,-,-,-,-,-,-
#> ENSG00000168309 -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
#> ENSG00000152583 -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
#> ENSG00000120129 -,-,-,-
#> ENSG00000189221 +,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+
#> ENSG00000146250 +,+,+,+,+
#> ENSG00000171819 +,+,+,+,+,+,+,+
#> ENSG00000157214 +,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+
#> exon_id
#> ENSG00000109906 360958,360959,360960,360961,360962,360963,360964,360965,360967,360966,360968,360969,360971,360970,360972,360974,360973,360975,360976,360977,360978,360979,360980,360981,360982,360983,360984,360985,360986,360987
#> ENSG00000165995 321791,321792,321793,321794,321795,321796,321797,321798,321799,321800,321801,321802,321803,321804,321805,321806,321807,321808,321809,321810,321811,321812,321813,321814,321815,321816,321817,321818,321819,321820,321821,321822,321823,321824
#> ENSG00000250978 199128,199130,199131,199132,199133,199134,199135
#> ENSG00000168309 140728,140729,140730,140731,140732,140733,140734,140735,140736,140737,140738,140739,140741,140740,140742,140743,140744,140745
#> ENSG00000152583 172689,172690,172691,172692,172693,172694,172695,172696,172697,172699,172698,172700,172701,172702,172703,172704,172705,172707,172706,172708,172709,172710,172711,172712,172713,172714,172715,172716,172717,172718,172719,172720,172721,172722,172723,172724,172725,172726,172727
#> ENSG00000120129 207637,207638,207639,207640
#> ENSG00000189221 653982,653983,653984,653985,653986,653987,653989,653988,653990,653991,653992,653993,653994,653995,653996,653997,653998,653999,654000,654001,654002,654003,654004,654005,654006,654007,654008,654009,654010
#> ENSG00000146250 218407,218408,218409,218410,218411
#> ENSG00000171819 2221,2222,2223,2224,2225,2226,2227,2228
#> ENSG00000157214 246728,246730,246731,246732,246733,246734,246735,246736,246737,246738,246739,246740,246741,246743,246742,246744,246745,246746,246747,246748,246749,246750,246751,246752,246753,246754,246755
#> exon_name
#> ENSG00000109906 ENSE00001344383,ENSE00002217296,ENSE00002239785,ENSE00002278969,ENSE00001777728,ENSE00002277816,ENSE00002264739,ENSE00002267450,ENSE00003532715,ENSE00003522546,ENSE00002223922,ENSE00002239280,ENSE00003606532,ENSE00003503866,ENSE00002304588,ENSE00003667676,ENSE00003652618,ENSE00002237247,ENSE00002308595,ENSE00003574983,ENSE00003648066,ENSE00002216844,ENSE00002254046,ENSE00002202712,ENSE00003533854,ENSE00003675344,ENSE00002251269,ENSE00002289800,ENSE00002238115,ENSE00001513888
#> ENSG00000165995 ENSE00001552836,ENSE00001323316,ENSE00001912501,ENSE00001877551,ENSE00001563168,ENSE00001473561,ENSE00003566244,ENSE00003685211,ENSE00001824310,ENSE00001935997,ENSE00001473551,ENSE00001696833,ENSE00001402115,ENSE00001811759,ENSE00001473523,ENSE00003471380,ENSE00003510985,ENSE00001005446,ENSE00001886774,ENSE00001005448,ENSE00001005464,ENSE00001005450,ENSE00001367687,ENSE00001385143,ENSE00001098801,ENSE00001098797,ENSE00001098795,ENSE00001098805,ENSE00001737387,ENSE00001098799,ENSE00001266433,ENSE00001846919,ENSE00001548772,ENSE00001552865
#> ENSG00000250978 ENSE00002085457,ENSE00002055881,ENSE00002051029,ENSE00002080371,ENSE00002028106,ENSE00002048405,ENSE00002074015
#> ENSG00000168309 ENSE00001419495,ENSE00001913711,ENSE00001833888,ENSE00001891124,ENSE00001228325,ENSE00001929708,ENSE00003652265,ENSE00003666445,ENSE00001518622,ENSE00001876866,ENSE00001518624,ENSE00001736715,ENSE00003684332,ENSE00003505632,ENSE00001872799,ENSE00001849960,ENSE00001901828,ENSE00001854286
#> ENSG00000152583 ENSE00001914146,ENSE00001135423,ENSE00002056886,ENSE00001175672,ENSE00001175678,ENSE00001175684,ENSE00001175691,ENSE00001006057,ENSE00001006053,ENSE00003651115,ENSE00003561541,ENSE00003487906,ENSE00003598972,ENSE00001786211,ENSE00002316459,ENSE00002028083,ENSE00001789990,ENSE00003602905,ENSE00003459209,ENSE00002234840,ENSE00001678790,ENSE00002045268,ENSE00003592507,ENSE00003613792,ENSE00001605148,ENSE00002310772,ENSE00002225747,ENSE00002211631,ENSE00002063937,ENSE00002061881,ENSE00002270604,ENSE00002252787,ENSE00002269371,ENSE00001175712,ENSE00001603831,ENSE00001942085,ENSE00002020252,ENSE00002083738,ENSE00002034086
#> ENSG00000120129 ENSE00001876542,ENSE00000769464,ENSE00000769465,ENSE00000812856
#> ENSG00000189221 ENSE00001415055,ENSE00002218265,ENSE00001834008,ENSE00001836223,ENSE00003501661,ENSE00003656032,ENSE00003691177,ENSE00003550793,ENSE00003487993,ENSE00003504764,ENSE00003590154,ENSE00003495252,ENSE00003524833,ENSE00003526715,ENSE00003672501,ENSE00001811266,ENSE00001383783,ENSE00001382812,ENSE00001377890,ENSE00001373498,ENSE00001369566,ENSE00001677475,ENSE00001816354,ENSE00001614970,ENSE00003583432,ENSE00003609031,ENSE00001875207,ENSE00002311052,ENSE00001389556
#> ENSG00000146250 ENSE00002225101,ENSE00001450675,ENSE00002300058,ENSE00002228069,ENSE00001450674
#> ENSG00000171819 ENSE00001471825,ENSE00001168153,ENSE00001168146,ENSE00001948794,ENSE00001168140,ENSE00001823259,ENSE00001841505,ENSE00001471787
#> ENSG00000157214 ENSE00001600835,ENSE00001206871,ENSE00001519027,ENSE00001519061,ENSE00001622820,ENSE00002226827,ENSE00001547971,ENSE00001519060,ENSE00001519048,ENSE00001897780,ENSE00001519046,ENSE00001620946,ENSE00001752071,ENSE00003616543,ENSE00003474395,ENSE00001638606,ENSE00001938466,ENSE00001031278,ENSE00001275182,ENSE00001519045,ENSE00001519014,ENSE00001918233,ENSE00001845894,ENSE00003246458,ENSE00001779097,ENSE00001519026,ENSE00001553338
#> logFC logCPM F PValue FDR
#> ENSG00000109906 -7.133346 4.143740 1525.8323 2.153210e-13 1.371099e-08
#> ENSG00000165995 -3.275414 4.504348 1239.8936 9.820233e-13 3.126615e-08
#> ENSG00000250978 -6.158218 1.348282 398.1877 3.860048e-12 7.978739e-08
#> ENSG00000168309 -4.693470 2.775385 731.1744 5.830619e-12 7.978739e-08
#> ENSG00000152583 -4.547502 5.528678 884.7229 6.265009e-12 7.978739e-08
#> ENSG00000120129 -2.930350 7.308257 757.6713 1.462852e-11 1.552501e-07
#> ENSG00000189221 -3.323171 6.766776 713.3290 2.034469e-11 1.787243e-07
#> ENSG00000146250 2.764572 3.909086 700.7739 2.245386e-11 1.787243e-07
#> ENSG00000171819 -5.700790 3.500283 509.4399 2.818525e-11 1.896165e-07
#> ENSG00000157214 -1.961807 7.129056 644.5267 3.540253e-11 1.896165e-07# If you performed likelihood ratio tests
fit <- glmFit(y, design)
lrt <- glmLRT(fit)
topTags(lrt)#> Coefficient: dexuntrt
#> seqnames
#> ENSG00000109906 11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11
#> ENSG00000165995 10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10
#> ENSG00000152583 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4
#> ENSG00000171819 1,1,1,1,1,1,1,1
#> ENSG00000120129 5,5,5,5
#> ENSG00000189221 X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X,X
#> ENSG00000162692 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
#> ENSG00000168309 3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3
#> ENSG00000101347 20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20
#> ENSG00000127954 7,7,7,7,7,7,7,7,7,7
#> start
#> ENSG00000109906 113930315,113930447,113930459,113930979,113931229,113932093,113933933,113933933,113933933,113933933,113935134,113992540,114027059,114027059,114051488,114057674,114057674,114057674,114107929,114112889,114112889,114117512,114117920,114117920,114117920,114117920,114121048,114121048,114121048,114121048
#> ENSG00000165995 18429606,18429666,18429676,18429721,18429887,18430109,18439812,18439812,18439812,18470736,18549698,18550190,18629646,18629666,18689742,18690853,18690853,18787284,18787284,18789741,18795400,18803165,18803440,18803909,18807265,18807839,18816517,18823005,18825030,18827109,18828159,18828159,18828159,18828159
#> ENSG00000152583 88394487,88394500,88394570,88400582,88401524,88403576,88411425,88411912,88412770,88414734,88414734,88415521,88415521,88415528,88415569,88415592,88415685,88416133,88416133,88416133,88416165,88418283,88420673,88420673,88425974,88449278,88449707,88449707,88450197,88450197,88450197,88450197,88450197,88450197,88450197,88450197,88451697,88452130,88452130
#> ENSG00000171819 11249398,11252327,11253637,11253684,11254518,11254583,11254911,11254911
#> ENSG00000120129 172195093,172196578,172197164,172197589
#> ENSG00000189221 43515467,43515548,43515550,43517110,43542761,43542761,43552538,43552538,43571119,43571119,43571119,43571952,43571952,43587420,43587420,43590488,43590488,43590941,43591946,43595474,43599928,43601197,43602951,43603041,43603356,43603356,43603614,43603614,43603614
#> ENSG00000162692 101185298,101185311,101185316,101185320,101186032,101186032,101188576,101190180,101194663,101196754,101197974,101200058,101200731,101203679,101203679,101203679
#> ENSG00000168309 58549844,58551188,58551188,58551579,58552935,58552946,58555418,58555418,58556053,58563036,58563036,58572585,58574933,58574933,58594601,58612698,58612698,58613143
#> ENSG00000101347 35518632,35525971,35526225,35526843,35532560,35532560,35533767,35533767,35539621,35540751,35540864,35545125,35545352,35547767,35555585,35555585,35559163,35559163,35563432,35563432,35563744,35569442,35569442,35575141,35575141,35579839,35579839
#> ENSG00000127954 87905744,87907343,87910230,87910798,87911956,87913129,87920231,87936107,87936107,87936107
#> end
#> ENSG00000109906 113930604,113930604,113930604,113931016,113931306,113932283,113934368,113934466,113935290,113935290,113935290,113992636,114027156,114027156,114051664,114057760,114057760,114060486,114108062,114113059,114113059,114118087,114118018,114118066,114118087,114118087,114121198,114121279,114121374,114121398
#> ENSG00000165995 18429785,18429785,18429785,18429785,18430144,18430144,18439904,18439904,18440198,18471036,18550246,18550246,18629906,18629906,18690029,18690972,18690972,18787406,18787722,18789877,18795476,18803298,18803459,18803970,18807345,18807897,18816626,18823156,18825125,18827294,18828653,18830038,18830056,18830798
#> ENSG00000152583 88394955,88394955,88394955,88400730,88401672,88403712,88411545,88412030,88412842,88415750,88415750,88415750,88415750,88415750,88415750,88415750,88415750,88416279,88416279,88416295,88416279,88418391,88420737,88420737,88426075,88449385,88449766,88449771,88450244,88450253,88450393,88450524,88450556,88450609,88450655,88450656,88451783,88452201,88452213
#> ENSG00000171819 11250012,11252427,11253831,11253831,11254716,11254716,11255235,11256038
#> ENSG00000120129 172196135,172196797,172197309,172198198
#> ENSG00000189221 43515662,43515662,43515662,43517217,43542855,43542855,43552675,43552675,43571223,43571223,43571223,43572043,43572043,43587561,43587561,43590629,43590637,43591100,43592042,43595527,43599985,43601294,43603152,43603152,43603418,43603418,43603905,43604409,43606068
#> ENSG00000162692 101185480,101185480,101185480,101185480,101186121,101186307,101188896,101190446,101194938,101197074,101198240,101200324,101204595,101204169,101204594,101204601
#> ENSG00000168309 58552422,58552422,58553091,58552422,58553091,58553091,58555592,58555592,58556150,58563115,58563491,58572840,58574996,58574996,58594984,58613147,58613337,58613337
#> ENSG00000101347 35521469,35526362,35526362,35526947,35532652,35532652,35533797,35533906,35539736,35540955,35540955,35545233,35545452,35547922,35555655,35555655,35559278,35559278,35563592,35563592,35563806,35569514,35569514,35575207,35575207,35580111,35580246
#> ENSG00000127954 87908943,87908943,87910394,87912483,87912483,87913586,87920329,87936195,87936203,87936206
#> width
#> ENSG00000109906 290,158,146,38,78,191,436,534,1358,1358,157,97,98,98,177,87,87,2813,134,171,171,576,99,147,168,168,151,232,327,351
#> ENSG00000165995 180,120,110,65,258,36,93,93,387,301,549,57,261,241,288,120,120,123,439,137,77,134,20,62,81,59,110,152,96,186,495,1880,1898,2640
#> ENSG00000152583 469,456,386,149,149,137,121,119,73,1017,1017,230,230,223,182,159,66,147,147,163,115,109,65,65,102,108,60,65,48,57,197,328,360,413,459,460,87,72,84
#> ENSG00000171819 615,101,195,148,199,134,325,1128
#> ENSG00000120129 1043,220,146,610
#> ENSG00000189221 196,115,113,108,95,95,138,138,105,105,105,92,92,142,142,142,150,160,97,54,58,98,202,112,63,63,292,796,2455
#> ENSG00000162692 183,170,165,161,90,276,321,267,276,321,267,267,3865,491,916,923
#> ENSG00000168309 2579,1235,1904,844,157,146,175,175,98,80,456,256,64,64,384,450,640,195
#> ENSG00000101347 2838,392,138,105,93,93,31,140,116,205,92,109,101,156,71,71,116,116,161,161,63,73,73,67,67,273,408
#> ENSG00000127954 3200,1601,165,1686,528,458,99,89,97,100
#> strand
#> ENSG00000109906 +,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+
#> ENSG00000165995 +,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+
#> ENSG00000152583 -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
#> ENSG00000171819 +,+,+,+,+,+,+,+
#> ENSG00000120129 -,-,-,-
#> ENSG00000189221 +,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+
#> ENSG00000162692 +,+,+,+,+,+,+,+,+,+,+,+,+,+,+,+
#> ENSG00000168309 -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
#> ENSG00000101347 -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
#> ENSG00000127954 -,-,-,-,-,-,-,-,-,-
#> exon_id
#> ENSG00000109906 360958,360959,360960,360961,360962,360963,360964,360965,360967,360966,360968,360969,360971,360970,360972,360974,360973,360975,360976,360977,360978,360979,360980,360981,360982,360983,360984,360985,360986,360987
#> ENSG00000165995 321791,321792,321793,321794,321795,321796,321797,321798,321799,321800,321801,321802,321803,321804,321805,321806,321807,321808,321809,321810,321811,321812,321813,321814,321815,321816,321817,321818,321819,321820,321821,321822,321823,321824
#> ENSG00000152583 172689,172690,172691,172692,172693,172694,172695,172696,172697,172699,172698,172700,172701,172702,172703,172704,172705,172707,172706,172708,172709,172710,172711,172712,172713,172714,172715,172716,172717,172718,172719,172720,172721,172722,172723,172724,172725,172726,172727
#> ENSG00000171819 2221,2222,2223,2224,2225,2226,2227,2228
#> ENSG00000120129 207637,207638,207639,207640
#> ENSG00000189221 653982,653983,653984,653985,653986,653987,653989,653988,653990,653991,653992,653993,653994,653995,653996,653997,653998,653999,654000,654001,654002,654003,654004,654005,654006,654007,654008,654009,654010
#> ENSG00000162692 14792,14793,14794,14795,14796,14797,14798,14799,14800,14801,14802,14803,14804,14805,14806,14807
#> ENSG00000168309 140728,140729,140730,140731,140732,140733,140734,140735,140736,140737,140738,140739,140741,140740,140742,140743,140744,140745
#> ENSG00000101347 626560,626561,626562,626563,626565,626564,626566,626567,626568,626569,626570,626571,626572,626573,626575,626574,626576,626577,626578,626579,626580,626581,626582,626584,626583,626585,626586
#> ENSG00000127954 263537,263538,263539,263540,263541,263542,263543,263544,263545,263546
#> exon_name
#> ENSG00000109906 ENSE00001344383,ENSE00002217296,ENSE00002239785,ENSE00002278969,ENSE00001777728,ENSE00002277816,ENSE00002264739,ENSE00002267450,ENSE00003532715,ENSE00003522546,ENSE00002223922,ENSE00002239280,ENSE00003606532,ENSE00003503866,ENSE00002304588,ENSE00003667676,ENSE00003652618,ENSE00002237247,ENSE00002308595,ENSE00003574983,ENSE00003648066,ENSE00002216844,ENSE00002254046,ENSE00002202712,ENSE00003533854,ENSE00003675344,ENSE00002251269,ENSE00002289800,ENSE00002238115,ENSE00001513888
#> ENSG00000165995 ENSE00001552836,ENSE00001323316,ENSE00001912501,ENSE00001877551,ENSE00001563168,ENSE00001473561,ENSE00003566244,ENSE00003685211,ENSE00001824310,ENSE00001935997,ENSE00001473551,ENSE00001696833,ENSE00001402115,ENSE00001811759,ENSE00001473523,ENSE00003471380,ENSE00003510985,ENSE00001005446,ENSE00001886774,ENSE00001005448,ENSE00001005464,ENSE00001005450,ENSE00001367687,ENSE00001385143,ENSE00001098801,ENSE00001098797,ENSE00001098795,ENSE00001098805,ENSE00001737387,ENSE00001098799,ENSE00001266433,ENSE00001846919,ENSE00001548772,ENSE00001552865
#> ENSG00000152583 ENSE00001914146,ENSE00001135423,ENSE00002056886,ENSE00001175672,ENSE00001175678,ENSE00001175684,ENSE00001175691,ENSE00001006057,ENSE00001006053,ENSE00003651115,ENSE00003561541,ENSE00003487906,ENSE00003598972,ENSE00001786211,ENSE00002316459,ENSE00002028083,ENSE00001789990,ENSE00003602905,ENSE00003459209,ENSE00002234840,ENSE00001678790,ENSE00002045268,ENSE00003592507,ENSE00003613792,ENSE00001605148,ENSE00002310772,ENSE00002225747,ENSE00002211631,ENSE00002063937,ENSE00002061881,ENSE00002270604,ENSE00002252787,ENSE00002269371,ENSE00001175712,ENSE00001603831,ENSE00001942085,ENSE00002020252,ENSE00002083738,ENSE00002034086
#> ENSG00000171819 ENSE00001471825,ENSE00001168153,ENSE00001168146,ENSE00001948794,ENSE00001168140,ENSE00001823259,ENSE00001841505,ENSE00001471787
#> ENSG00000120129 ENSE00001876542,ENSE00000769464,ENSE00000769465,ENSE00000812856
#> ENSG00000189221 ENSE00001415055,ENSE00002218265,ENSE00001834008,ENSE00001836223,ENSE00003501661,ENSE00003656032,ENSE00003691177,ENSE00003550793,ENSE00003487993,ENSE00003504764,ENSE00003590154,ENSE00003495252,ENSE00003524833,ENSE00003526715,ENSE00003672501,ENSE00001811266,ENSE00001383783,ENSE00001382812,ENSE00001377890,ENSE00001373498,ENSE00001369566,ENSE00001677475,ENSE00001816354,ENSE00001614970,ENSE00003583432,ENSE00003609031,ENSE00001875207,ENSE00002311052,ENSE00001389556
#> ENSG00000162692 ENSE00001167786,ENSE00001811760,ENSE00001825682,ENSE00001451872,ENSE00001451878,ENSE00001067757,ENSE00001067755,ENSE00001067758,ENSE00001067756,ENSE00001067753,ENSE00001067759,ENSE00001067751,ENSE00003565397,ENSE00001892498,ENSE00001451871,ENSE00001167778
#> ENSG00000168309 ENSE00001419495,ENSE00001913711,ENSE00001833888,ENSE00001891124,ENSE00001228325,ENSE00001929708,ENSE00003652265,ENSE00003666445,ENSE00001518622,ENSE00001876866,ENSE00001518624,ENSE00001736715,ENSE00003684332,ENSE00003505632,ENSE00001872799,ENSE00001849960,ENSE00001901828,ENSE00001854286
#> ENSG00000101347 ENSE00000800455,ENSE00001930417,ENSE00000661812,ENSE00000661813,ENSE00003692177,ENSE00003551249,ENSE00001842453,ENSE00000661815,ENSE00001622813,ENSE00001604475,ENSE00001711142,ENSE00001793017,ENSE00001667406,ENSE00001752622,ENSE00003598833,ENSE00003555165,ENSE00003535434,ENSE00003608826,ENSE00003546823,ENSE00003559540,ENSE00002218059,ENSE00003462531,ENSE00003673643,ENSE00003619308,ENSE00003541183,ENSE00001957470,ENSE00001898623
#> ENSG00000127954 ENSE00001917465,ENSE00001277946,ENSE00001163797,ENSE00001753614,ENSE00001483677,ENSE00001120706,ENSE00001621319,ENSE00001673636,ENSE00001905312,ENSE00001871078
#> logFC logCPM LR PValue FDR
#> ENSG00000109906 -7.142190 4.143740 1277.6447 8.154169e-280 5.192330e-275
#> ENSG00000165995 -3.274796 4.504348 826.0713 1.158242e-181 3.687670e-177
#> ENSG00000152583 -4.554996 5.528678 693.6567 7.163187e-153 1.520434e-148
#> ENSG00000171819 -5.666372 3.500283 602.1496 5.704778e-133 9.081579e-129
#> ENSG00000120129 -2.932425 7.308257 554.3550 1.421037e-122 1.809747e-118
#> ENSG00000189221 -3.336778 6.766776 544.9495 1.580103e-120 1.676937e-116
#> ENSG00000162692 3.686533 4.599336 530.9701 1.737408e-117 1.580471e-113
#> ENSG00000168309 -4.723461 2.775385 505.4801 6.103995e-112 4.858551e-108
#> ENSG00000101347 -3.751832 9.206504 498.2099 2.330547e-110 1.648914e-106
#> ENSG00000127954 -5.175401 3.652849 491.7830 5.832387e-109 3.713889e-105# lrt to DESeqResults
tbledger <- lrt$table
colnames(tbledger)[colnames(tbledger) == "PValue"] <- "pvalue"
colnames(tbledger)[colnames(tbledger) == "logFC"] <- "log2FoldChange"
colnames(tbledger)[colnames(tbledger) == "logCPM"] <- "baseMean"
# get from the logcpm to something more the baseMean for better
tbledger$baseMean <- (2^tbledger$baseMean) * mean(dge_airway$samples$lib.size) / 1e6
# use the constructor for DESeqResults
edger_resu <- DESeqResults(DataFrame(tbledger))
edger_resu <- DESeq2:::pvalueAdjustment(edger_resu,
independentFiltering = TRUE,
alpha = 0.05, pAdjustMethod = "BH"
)
# cfr with res_airway
# plot(res_airway$pvalue,edger_resu$pvalue)
### with limma-voom
x <- calcNormFactors(dge_airway)
design <- model.matrix(~ 0 + dex + cell)
contr.matrix <- makeContrasts(dextrt - dexuntrt, levels = colnames(design))
v <- voom(x, design)
vfit <- lmFit(v, design)
vfit <- contrasts.fit(vfit, contrasts = contr.matrix)
efit <- eBayes(vfit)
tbllimma <- topTable(efit, number = Inf, sort.by = "none")
colnames(tbllimma)[colnames(tbllimma) == "P.Value"] <- "pvalue"
colnames(tbllimma)[colnames(tbllimma) == "logFC"] <- "log2FoldChange"
colnames(tbllimma)[colnames(tbllimma) == "AveExpr"] <- "baseMean"
colnames(tbllimma)[colnames(tbllimma) == "adj.P.Val"] <- "padj"
# get from the logcpm to something more the baseMean for better
tbllimma$baseMean <- (2^tbllimma$baseMean) * mean(dge_airway$samples$lib.size) / 1e6
# use the constructor for DESeqResults
limma_resu <- DESeqResults(DataFrame(tbllimma))
# cfr with res_airway
# plot(res_airway$pvalue,limma_resu$pvalue)After preparing the objects, you can launch the app with the following command:
ideal(redo_dds_airway, edger_resu)
# or ...
ideal(redo_dds_airway, limma_resu)Basically, you need a data.frame (e.g. myresults_df) with 3 columns to create the DESeqResults object to be passed to the app, with this names:
baseMeanas an average expression valuelog2FoldChangeas an indicator for the effect sizepvalueas a measure of significance
Then, you just need to call DESeqResults(DataFrame(myresults_df)).padj can be computed either by p.adjust or using DESeq2:::pvalueAdjustment as in the example above.