### R code from vignette source 'vignettes/ToPASeq/inst/doc/ToPASeq.Rnw'
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### code chunk number 1: ToPASeq.Rnw:80-81
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options(width=60)
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### code chunk number 2: lib
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library(ToPASeq)
library(DEGraph)
data(Loi2008_DEGraphVignette)
pathways<-kegg[1:5]
ls()
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### code chunk number 3: ToPASeq.Rnw:101-130 (eval = FALSE)
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## top<-TopologyGSA(exprLoi2008, classLoi2008, pathways, type="MA", nperm=200)
## #99 node labels mapped to the expression data
## #Average coverage 31.47657 %
## #0 (out of 5) pathways without a mapped node
## #Acute myeloid leukemia
## #Adherens junction
## #Adipocytokine signaling pathway
## #Adrenergic signaling in cardiomyocytes
## #African trypanosomiasis
## res(top)
## # t.value df.mean1 df.mean2 p.value
## #Acute myeloid leukemia 3080.663 30 224 0.000
## #Adherens junction 1102.830 10 244 0.040
## #Adipocytokine signaling pathway 3196.432 25 229 0.000
## #Adrenergic signaling in cardiomyocytes 2178.476 26 228 0.055
## #African trypanosomiasis 1400.088 8 246 0.000
## # lambda.value df.var p.value.var
## #Acute myeloid leukemia 217.92044 165 3.622794e-03
## #Adherens junction 39.92094 10 1.749659e-05
## #Adipocytokine signaling pathway 192.81336 121 3.595452e-05
## #Adrenergic signaling in cardiomyocytes 169.47418 80 2.211953e-08
## #African trypanosomiasis 13.77192 15 5.428926e-01
## # qchisq.value var.equal
## #Acute myeloid leukemia 195.97336 1
## #Adherens junction 18.30704 1
## #Adipocytokine signaling pathway 147.67353 1
## #Adrenergic signaling in cardiomyocytes 101.87947 1
## #African trypanosomiasis 24.99579 0
##
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### code chunk number 4: ToPASeq.Rnw:140-142
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deg<-DEGraph(exprLoi2008, classLoi2008, pathways, type="MA")
res(deg)
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### code chunk number 5: ToPASeq.Rnw:153-187 (eval = FALSE)
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## cli<-Clipper( exprLoi2008, classLoi2008, pathways,type="MA", test="mean")
## #99 node labels mapped to the expression data
## #Average coverage 31.47657 %
## #0 (out of 5) pathways without a mapped node
## #Acute myeloid leukemia
## #Adherens junction
## #Adipocytokine signaling pathway
## #Adrenergic signaling in cardiomyocytes
## #African trypanosomiasis
## res(cli)
## # alphaVar alphaMean maxScore activation
## #Acute myeloid leukemia 0.788 0.008 4.336307 0.1255490
## #Adherens junction 0.087 0.027 NA NA
## #Adipocytokine signaling pathway 0.675 0.000 33.209403 0.8012589
## #Adrenergic signaling in cardiomyocytes 0.108 0.042 NA NA
## #African trypanosomiasis 0.966 0.005 NA NA
## # impact
## #Acute myeloid leukemia 0.3846154
## #Adherens junction NA
## #Adipocytokine signaling pathway 0.5000000
## #Adrenergic signaling in cardiomyocytes NA
## #African trypanosomiasis NA
## # involvedGenes
## #Acute myeloid leukemia 2475;6199;1978;2475;2475;6198
## #Adherens junction NA
## #Adipocytokine signaling pathway 32;51422;53632;5562;5563;5564;5565;5571;2538;51422;53632;5562;5563;5564;5565;5571;5105;51422;53632;5562;5563;5564;5565;5571;5106;51422;53632;5562;5563;5564;5565;5571;51422;53632;5562;5563;5564;5565;5571;57818;51422;53632;5562;5563;5564;5565;5571;6517
## #Adrenergic signaling in cardiomyocytes NA
## #African trypanosomiasis NA
## # pathGenes
## #Acute myeloid leukemia 10000;207;208;23533;3265;3845;4893;5290;5291;5293;5294;5295;5296;8503,10000;207;208;2475,2475;6199,1978;2475,2475;6198
## #Adherens junction NA
## #Adipocytokine signaling pathway 32;51422;53632;5562;5563;5564;5565;5571,2538;51422;53632;5562;5563;5564;5565;5571,5105;51422;53632;5562;5563;5564;5565;5571,5106;51422;53632;5562;5563;5564;5565;5571,51422;53632;5562;5563;5564;5565;5571;57818,51422;53632;5562;5563;5564;5565;5571;6517
## #Adrenergic signaling in cardiomyocytes NA
## #African trypanosomiasis NA
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### code chunk number 6: ToPASeq.Rnw:196-198
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spi<-SPIA(exprLoi2008, classLoi2008,pathways , type="MA", logFC.th=-1)
res(spi)
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### code chunk number 7: ToPASeq.Rnw:206-208
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tap<-TAPPA(exprLoi2008, classLoi2008, pathways, type="MA")
res(tap)
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### code chunk number 8: ToPASeq.Rnw:217-238 (eval = FALSE)
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## tbs<-TBS( exprLoi2008, classLoi2008, pathways, type="MA", logFC.th=-1, nperm=100)
## #99 node labels mapped to the expression data
## #Average coverage 31.47657 %
## #0 (out of 5) pathways without a mapped node
## #0 denoted as 0
## # 1 denoted as 1
## # Contrasts: 0 - 1
## #Found 40 differentially expressed genes
## #Preparing permutation table and downstream list
## #Observed scores..
## #Random scores..
## #100
## #Normalization and p-values...
## res(tbs)
## # TBS.obs.norm p p.adj
## #Acute myeloid leukemia -0.8012546 0.90 0.9000000
## #Adherens junction 2.9052652 0.03 0.1250000
## #Adipocytokine signaling pathway 0.8461749 0.10 0.1666667
## #Adrenergic signaling in cardiomyocytes -0.5548923 0.80 0.9000000
## #African trypanosomiasis 1.5028307 0.05 0.1250000
##
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### code chunk number 9: ToPASeq.Rnw:246-268 (eval = FALSE)
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## pwe<-PWEA(exprLoi2008, classLoi2008, pathways, type="MA", nperm=100)
## #99 node labels mapped to the expression data
## #Average coverage 31.47657 %
## #0 (out of 5) pathways without a mapped node
## #0 denoted as 0
## # 1 denoted as 1
## # Contrasts: 0 - 1
## #Preparing data..
## #100
## #Processing gene set:
## #Acute myeloid leukemia
## #Adherens junction
## #Adipocytokine signaling pathway
## #Adrenergic signaling in cardiomyocytes
## #African trypanosomiasis
## res(pwe)
## # ES p p.adj
## #Acute myeloid leukemia 0.1995347 0.81 0.81
## #Adherens junction 0.5757274 0.67 0.81
## #Adipocytokine signaling pathway 0.3272288 0.32 0.81
## #Adrenergic signaling in cardiomyocytes 0.3888446 0.68 0.81
## #African trypanosomiasis 0.3544996 0.46 0.81
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### code chunk number 10: ToPASeq.Rnw:280-285
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library(gageData)
data(hnrnp.cnts)
hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,]
group<-c(rep("sample",4), rep("control",4))
pathways<-kegg[1:10]
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### code chunk number 11: ToPASeq.Rnw:296-315 (eval = FALSE)
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## top<-TopologyGSA(hnrnp.cnts, group, pathways[1:3], type="RNASeq", nperm=1000)
## #528 node labels mapped to the expression data
## #Average coverage 83.16538
## #0 (out of 10) pathways without a mapped node
## #Normalization method was not specified. TMM used as default
## #Acute myeloid leukemia
## #Adherens junction
## #Adipocytokine signaling pathway
## #Adrenergic signaling in cardiomyocytes
## #African trypanosomiasis
## #Alanine, aspartate and glutamate metabolism
## #Aldosterone-regulated sodium reabsorption
## #Allograft rejection
## #alpha-Linolenic acid metabolism
##
## res(top)
## #data frame with 0 columns and 1 rows
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##
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### code chunk number 12: ToPASeq.Rnw:327-329
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deg<-DEGraph(hnrnp.cnts, group, pathways, type="RNASeq")
res(deg)[,1:4]
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### code chunk number 13: ToPASeq.Rnw:340-362 (eval = FALSE)
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## cli<-Clipper(hnrnp.cnts, group, pathways, type="RNASeq", test="mean")
## #528 node labels mapped to the expression data
## #Average coverage 83.16538
## #0 (out of 10) pathways without a mapped node
## #Normalization method was not specified. TMM used as default
## #Acute myeloid leukemia
## #Adherens junction
## #Adipocytokine signaling pathway
## #Adrenergic signaling in cardiomyocytes
## #African trypanosomiasis
## #Alanine, aspartate and glutamate metabolism
## #Alcoholism
## #Aldosterone-regulated sodium reabsorption
## #Allograft rejection
## #alpha-Linolenic acid metabolism
## res(cli)[1:2,]
## # alphaVar alphaMean maxScore activation impact involvedGenes
## #Acute myeloid leukemia 0.022 0.008 18.290959 0.3782696 0.2592593 3728;4609;3728;5467;3728;595;3728;6932;3728;6934;3728;83439
## #Adherens junction 0.035 0.018 1.956012 0.1415808 0.1052632 4087;4088;4089;7046;7048
## # pathGenes
## #Acute myeloid leukemia 3728;5371;5914;861,3728;4609,3728;5467,3728;595,3728;6932,3728;6934,3728;83439
## #Adherens junction 2260;6615;7046;7048,4087;4088;4089;7046;7048
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### code chunk number 14: ToPASeq.Rnw:371-373
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spi<-SPIA(hnrnp.cnts, group, pathways, type="RNASeq", logFC.th=-1)
res(spi)
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### code chunk number 15: ToPASeq.Rnw:381-383
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tap<-TAPPA(hnrnp.cnts, group, pathways, type="RNASeq")
res(tap)
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### code chunk number 16: ToPASeq.Rnw:392-415 (eval = FALSE)
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## tbs<-TBS(hnrnp.cnts, group, pathways, type="RNASeq", logFC.th=-1, nperm=100)
## #528 node labels mapped to the expression data
## #Average coverage 83.16538
## #0 (out of 10) pathways without a mapped node
## #test was not specified. 'vstlimma' used as default
## #Found 5702 differentially expressed genes
## #Preparing permutation table and downstream list
## #Observed scores..
## #Random scores..
## #100
## #Normalization and p-values...
## res(tbs)
## # TBS.obs.norm p p.adj
## #Acute myeloid leukemia -1.6325413 0.05 0.06250000
## #Adherens junction -3.9416308 0.01 0.01666667
## #Adipocytokine signaling pathway -3.1989858 0.00 0.00000000
## #Adrenergic signaling in cardiomyocytes -16.1777366 0.00 0.00000000
## #African trypanosomiasis -4.0834773 0.00 0.00000000
## #Alanine, aspartate and glutamate metabolism 0.0137086 0.44 0.48888889
## #Alcoholism -4.1997338 0.00 0.00000000
## #Aldosterone-regulated sodium reabsorption 1.9996012 1.00 1.00000000
## #Allograft rejection -3.4004380 0.01 0.01666667
## #alpha-Linolenic acid metabolism -2.6720346 0.02 0.02857143 0.0000000
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### code chunk number 17: ToPASeq.Rnw:423-452 (eval = FALSE)
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## pwe<-PWEA(hnrnp.cnts, group, pathways, type="RNASeq", nperm=100)
## #528 node labels mapped to the expression data
## #Average coverage 83.16538
## #0 (out of 10) pathways without a mapped node
## #test was not specified. 'vstlimma' used as default
## #Preparing data..
## #1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 Processing gene set:
## #Acute myeloid leukemia
## #Adherens junction
## #Adipocytokine signaling pathway
## #Adrenergic signaling in cardiomyocytes
## #African trypanosomiasis
## #Alanine, aspartate and glutamate metabolism
## #Alcoholism
## #Aldosterone-regulated sodium reabsorption
## #Allograft rejection
## #alpha-Linolenic acid metabolism
## res(pwe)
## # ES p p.adj
## #Acute myeloid leukemia 0.3526104 0.29 0.4142857
## #Adherens junction 0.3829831 1.00 1.0000000
## #Adipocytokine signaling pathway 0.3102945 1.00 1.0000000
## #Adrenergic signaling in cardiomyocytes 0.3611207 0.20 0.3333333
## #African trypanosomiasis 0.3272899 0.20 0.3333333
## #Alanine, aspartate and glutamate metabolism 0.2720946 0.20 0.3333333
## #Alcoholism 0.4708293 0.86 1.0000000
## #Aldosterone-regulated sodium reabsorption 0.3951037 0.20 0.3333333
## #Allograft rejection 0.9421248 0.03 0.3000000
## #alpha-Linolenic acid metabolism 0.6587026 0.20 0.3333333
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### code chunk number 18: ToPASeq.Rnw:473-482
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library(gageData)
data(hnrnp.cnts)
group<-c(rep("sample",4), rep("control",4))
hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,]
cli<-Clipper(hnrnp.cnts, group, kegg[1:2], type="RNASeq", testCliques=TRUE)
plot(cli,1, kegg)
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### code chunk number 19: ToPASeq.Rnw:492-500 (eval = FALSE)
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## library(gageData)
## data(hnrnp.cnts)
##
## group<-c(rep("sample",4), rep("control",4))
## hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,]
## spi<-SPIA(hnrnp.cnts, group, kegg[45:50], type="RNASeq", logFC.th=-1)
## plot(spi,"Complement and coagulation cascades", kegg[45:50], fontsize=50)
##