### R code from vignette source 'ToPASeq.Rnw' ################################################### ### code chunk number 1: ToPASeq.Rnw:66-70 ################################################### library(ToPASeq) pathways<-pathways("hsapiens", "kegg")[1:5] pathways[[1]] str(pathways[[1]]) ################################################### ### code chunk number 2: ToPASeq.Rnw:120-121 ################################################### options(width=60) ################################################### ### code chunk number 3: lib ################################################### library(ToPASeq) library(DEGraph) data(Loi2008_DEGraphVignette) pathways<-pathways("hsapiens", "kegg")[1:5] ls() ################################################### ### code chunk number 4: ToPASeq.Rnw:142-174 (eval = FALSE) ################################################### ## top<-TopologyGSA(exprLoi2008, classLoi2008, pathways, type="MA", perms=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) ## #$results ## # t.value df.mean1 df.mean2 p.value ## #Acute myeloid leukemia 3024.796 30 224 0 ## #Adherens junction 1102.830 10 244 0 ## #Adipocytokine signaling pathway 3196.432 25 229 0 ## #Adrenergic signaling in cardiomyocytes 2178.476 26 228 0 ## #African trypanosomiasis 1404.259 8 246 0 ## # lambda.value df.var p.value.var ## #Acute myeloid leukemia 213.01437 156 1.649509e-03 ## #Adherens junction 39.92094 10 1.749659e-05 ## #Adipocytokine signaling pathway 192.81336 121 3.595452e-05 ## #Adrenergic signaling in cardiomyocytes 169.47418 80 2.211953e-08 ## #African trypanosomiasis 13.02808 12 3.670031e-01 ## # qchisq.value var.equal q.value ## #Acute myeloid leukemia 186.14575 1 0 ## #Adherens junction 18.30704 1 0 ## #Adipocytokine signaling pathway 147.67353 1 0 ## #Adrenergic signaling in cardiomyocytes 101.87947 1 0 ## #African trypanosomiasis 21.02607 0 0 ## # ## #$errors ## #named list() ################################################### ### code chunk number 5: ToPASeq.Rnw:184-186 ################################################### deg<-DEGraph(exprLoi2008, classLoi2008, pathways, type="MA") res(deg) ################################################### ### code chunk number 6: ToPASeq.Rnw:197-226 (eval = FALSE) ################################################### ## cli<-clipper( exprLoi2008, classLoi2008, pathways,type="MA", method="mean") ## #99 node labels mapped to the expression data ## #Average coverage 31.47657 % ## #0 (out of 5) pathways without a mapped node ## #0 pathways were filtered out ## #Analysing pathway: ## # ## #Acute myeloid leukemia ## #Adherens junction ## #Adipocytokine signaling pathway ## #Adrenergic signaling in cardiomyocytes ## #African trypanosomiasis ## #0 denoted as 0 ## # 1 denoted as 1 ## # Contrasts: 1 - 0 ## #Warning messages: ## #1: In getJunctionTreePaths(graph, root) : ## # The DAG presents cliques that are not connected. ## #2: In prunePaths(clipped, pruneLevel) : pathSummary is NULL ## #3: In getJunctionTreePaths(graph, root) : ## # The DAG presents cliques that are not connected. ## #4: In prunePaths(clipped, pruneLevel) : pathSummary is NULL ## res(cli)$results[[1]] ## # alphaVar alphaMean mean.q.value var.q.value ## #Acute myeloid leukemia 0.735 0.009 0.0150 0.91875 ## #Adherens junction 0.101 0.022 0.0275 0.26500 ## #Adipocytokine signaling pathway 0.656 0.001 0.0050 0.91875 ## #Adrenergic signaling in cardiomyocytes 0.106 0.061 0.0610 0.26500 ## #African trypanosomiasis 0.953 0.007 0.0150 0.95300 ################################################### ### code chunk number 7: ToPASeq.Rnw:237-239 ################################################### spi<-SPIA(exprLoi2008, classLoi2008,pathways , type="MA", logFC.th=-1) res(spi) ################################################### ### code chunk number 8: ToPASeq.Rnw:254-256 ################################################### tap<-TAPPA(exprLoi2008, classLoi2008, pathways, type="MA") res(tap) ################################################### ### code chunk number 9: ToPASeq.Rnw:265-268 ################################################### Prs<-PRS( exprLoi2008, classLoi2008, pathways, type="MA", logFC.th=-1, nperm=100) res(Prs) ################################################### ### code chunk number 10: ToPASeq.Rnw:284-304 (eval = FALSE) ################################################### ## pwe<-PWEA(exprLoi2008, classLoi2008, pathways, type="MA", nperm=100) ## #0 denoted as 0 ## # 1 denoted as 1 ## # Contrasts: 1 - 0 ## #29 node labels mapped to the expression data ## #Average coverage 5.752782 % ## #1 (out of 5) pathways without a mapped node ## #1 pathways were filtered out ## # Preparing permutations.. ## res(pwe) ## #$results ## # ES p.value q.value ## #Acute myeloid leukemia -0.1516072 0.36 0.5066667 ## #Adherens junction 0.2576037 1.00 1.0000000 ## #Adipocytokine signaling pathway 0.2221782 0.38 0.5066667 ## #Adrenergic signaling in cardiomyocytes -0.2265755 0.05 0.2000000 ## # ## #$errors ## #named list() ## ################################################### ### code chunk number 11: seq1 ################################################### library(gageData) data(hnrnp.cnts) hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,] group<-c(rep("sample",4), rep("control",4)) pathways<-pathways("hsapiens", "kegg") ################################################### ### code chunk number 12: seq2 (eval = FALSE) ################################################### ## top<-TopologyGSA(hnrnp.cnts, group, pathways[1:3], type="RNASeq", nperm=1000) ## #528 node labels mapped to the expression data ## #Average coverage 83.16538 ## #0 (out of 10) pathways without a mapped node ## #Normalization method was not specified. TMM used as default ## #Acute myeloid leukemia ## #Adherens junction ## #Adipocytokine signaling pathway ## ## ## res(top) ## #data frame with 0 columns and 1 rows ## ## ################################################### ### code chunk number 13: seq3 ################################################### deg<-DEGraph(hnrnp.cnts, group, pathways, type="RNASeq") res(deg)[[1]][[1]] ################################################### ### code chunk number 14: seq4 (eval = FALSE) ################################################### ## cli<-clipper(hnrnp.cnts, group, pathways, type="RNASeq", method="mean") ## #530 node labels mapped to the expression data ## #Average coverage 82.98681 % ## #0 (out of 10) pathways without a mapped node ## #1 pathways were filtered out ## #Analysing pathway: ## # ## #Acute myeloid leukemia ## #Adherens junction ## #Adipocytokine signaling pathway ## #Adrenergic signaling in cardiomyocytes ## #African trypanosomiasis ## #Alanine, aspartate and glutamate metabolism ## #Alcoholism ## #Aldosterone-regulated sodium reabsorption ## #Allograft rejection ## #alpha-Linolenic acid metabolism ## res(cli)$results[[1]][1:2,] ## # alphaVar alphaMean mean.q.value var.q.value ## #Acute myeloid leukemia 0.026 0.010 0.016 0.033 ## #Adherens junction 0.030 0.009 0.016 0.033 ## ################################################### ### code chunk number 15: seq5 ################################################### spi<-SPIA(hnrnp.cnts, group, pathways, type="RNASeq", logFC.th=-1) res(spi) ################################################### ### code chunk number 16: seq6 ################################################### tap<-TAPPA(hnrnp.cnts, group, pathways, type="RNASeq") res(tap) ################################################### ### code chunk number 17: seq7 ################################################### Prs<-PRS(hnrnp.cnts, group, pathways, type="RNASeq", logFC.th=-1, nperm=100) res(Prs) ################################################### ### code chunk number 18: seq8 (eval = FALSE) ################################################### ## 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 ## #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 ################################################### ### code chunk number 19: plot1 (eval = FALSE) ################################################### ## #Fails during check ## library(gageData) ## data(hnrnp.cnts) ## ## group<-c(rep("sample",4), rep("control",4)) ## hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,] ## res<-clipper(hnrnp.cnts, group, pathways[1:2], type="RNASeq", testCliques=TRUE) ## ## plot(res,1, pathways) ## ################################################### ### code chunk number 20: plot2 (eval = FALSE) ################################################### ## library(gageData) ## data(hnrnp.cnts) ## ## group<-c(rep("sample",4), rep("control",4)) ## hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,] ## pathways<-pathways("hsapiens", "kegg")[50:55] ## spi<-SPIA(hnrnp.cnts, group, pathways, type="RNASeq", logFC.th=-1) ## plot(spi,"Complement and coagulation cascades", pathways, fontsize=50) ##