Gene Expression Prediction
Calculate the soft thresholding power (beta)
# Set powers to sample
powers = c(c(1:10), seq(from = 12, to = 60, by = 4))
# Call the network topology analysis function
sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 0)
k <- softConnectivity(datE = datExpr, power = sft$powerEstimate)
# Plot the results:
par(mfrow = c(1, 2))
cex1 = 0.9
# Scale-free topology fit index as a function of the
# soft-thresholding power
plot(sft$fitIndices[, 1], -sign(sft$fitIndices[, 3]) * sft$fitIndices[,
2], xlab = "Soft Threshold (power)", ylab = "Scale Free Topology Model Fit,signed R^2",
type = "n", main = paste("Scale independence"))
text(sft$fitIndices[, 1], -sign(sft$fitIndices[, 3]) * sft$fitIndices[,
2], labels = powers, cex = cex1, col = "red")
# this line corresponds to using an R^2 cut-off of h
abline(h = 0.8, col = "red")
# Mean connectivity as a function of the soft-thresholding
# power
fig <- plot(sft$fitIndices[, 1], sft$fitIndices[, 5], xlab = "Soft Threshold (power)",
ylab = "Mean Connectivity", type = "n", main = paste("Mean connectivity"))
text(sft$fitIndices[, 1], sft$fitIndices[, 5], labels = powers,
cex = cex1, col = "red")
par(mfrow = c(1, 2))
hist(k)
scaleFreePlot(k, main = "Check Scale free topology\n")
Blockwise module detection
net = blockwiseModules(datExpr, maxBlockSize = 5000, power = 30,
TOMType = "unsigned", minModuleSize = 10, reassignThreshold = 0,
mergeCutHeight = 0.05, numericLabels = TRUE, pamRespectsDendro = FALSE,
saveTOMs = FALSE, verbose = 0)
# Plot the dendogram with color assignment
mergedColors = labels2colors(net$colors)
plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
"Module colors", dendroLabels = FALSE, hang = 0.03, addGuide = TRUE,
guideHang = 0.05)
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs
geneTree = net$dendrograms[[1]]
bwnet = blockwiseModules(datExpr, maxBlockSize = 5000, power = 30,
TOMType = "unsigned", minModuleSize = 10, reassignThreshold = 0,
mergeCutHeight = 0.05, numericLabels = TRUE, saveTOMs = FALSE,
verbose = 0)
# Relabel blockwise modules
bwLabels = matchLabels(bwnet$colors, moduleLabels)
# Labels to colors for plotting
bwModuleColors = labels2colors(bwLabels)
# Comapre the single block to the block-wise network
# analysis
plotDendroAndColors(geneTree, cbind(moduleColors, bwModuleColors),
c("Single", "Blockwise"), main = "Single block gene dendrogram and module colors",
dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05)
figure <- plotDendroAndColors(geneTree, bwModuleColors, "", main = "Single block gene dendrogram and module colors",
dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05)
class(figure)
## [1] "list"
Merging of modules whose expression profiles are very similar
# Merge modules whose expression profiles are very similar
# Calculate Eigengenes to quantify co-expression similarity
# of entire modules
MEList = moduleEigengenes(datExpr, colors = bwModuleColors)
MEs = MEList$eigengenes
# Calculate dissimilarity
MEDiss = 1 - cor(MEs)
# Cluster module eigengnes and Plot thhe results
METree = hclust(as.dist(MEDiss), method = "average")
plot(METree, main = "Clustering of module eigengenes", xlab = "",
sub = "")
# Create Height Cut
MEDissThres = 0.25
abline(h = MEDissThres, col = "red")
merge = mergeCloseModules(datExpr, bwModuleColors, cutHeight = MEDissThres,
verbose = 0)
mergedColors = merge$colors
mergedMEs = merge$newMEs
Plot clustereing among samples
# Cluster tress (check if any outliers existed among
# samples)
datExpr_tree <- hclust(dist(datExpr), method = "average")
par(mar = c(0, 5, 2, 0))
plot(datExpr_tree, main = "Sample clustering", sub = "", xlab = "",
cex.lab = 2, cex.axis = 1, cex.main = 1, cex.lab = 1, cex = 0.5)
# Verify epigenegenes of modules in both approaches are
# extremely similar First calculate the module eigengenes
# for first approches
singleBlockMEs = moduleEigengenes(datExpr, moduleColors)$eigengenes
blockwiseMEs = moduleEigengenes(datExpr, bwModuleColors)$eigengenes
Blockwise MEs
blockwiseMEs
## MEbrown MEgreen MEgreenyellow MEgrey
## AC_134_CB_4029_WL 0.28099271 0.17762993 0.35745452 0.21382890
## CB_4012_KING_KARAJAZSY_WL 0.07720230 0.16282592 0.14734618 0.07532540
## COKER_310_WL 0.05320141 0.17872810 0.06091009 0.09001582
## DP_393_WL 0.29758909 0.16806460 0.19078918 0.25225847
## DP_493_WL 0.05650348 0.21231596 0.02753383 0.11751658
## FELISTANA_UA_7_18_WL 0.34557298 0.25440391 0.29250143 0.32793108
## FM_958_WL 0.20028005 0.10191755 0.11562843 0.20828774
## FUNTUA_FT_5_WL 0.06824831 0.10306328 0.04446967 0.11434909
## LOCKETT_BXL_WL 0.03451882 0.34976797 0.04360175 0.05604114
## MEXICO_910_WL 0.16358879 0.10507742 0.14666339 0.13684164
## PD_3_WL 0.17163486 0.07126565 0.07928296 0.16261628
## PLAINS_WL 0.08671709 0.10513544 0.11040560 0.11336913
## TAM_86III_26_WL 0.12397072 0.12055752 0.17125654 0.11490349
## TAM_91C_34_WL 0.12587051 0.09007225 0.22075697 0.12193630
## TAM_94WE_37S_WL 0.15349417 0.10921840 0.12413162 0.17096076
## VIR_6615_MCU_5_WL 0.11899688 0.06452298 0.02851864 0.11516948
## VIR_7065_ALLEN_333_WL 0.16379918 0.21414369 0.22066380 0.13448120
## VIR_7094_Coker_310_WL 0.04240716 0.12460396 0.04437249 0.11585341
## VIR_7153_D_10_WL 0.19419363 0.02608695 0.12407493 0.11432095
## VIR_7223_WL 0.15677910 0.22807984 0.32251528 0.17996851
## WESTERN_STORMPROOF_WL 0.01241071 0.05799473 -0.02432269 0.07872304
## AC_134_CB_4029_WW -0.18167593 -0.12796531 -0.16452395 -0.23253689
## CB_4012_KING_KARAJAZSY_WW -0.05842519 -0.10233020 -0.04542255 -0.04329441
## COKER_310_WW -0.07854541 -0.14687597 -0.12146514 -0.13760215
## DP_393_WW -0.11536056 -0.18398996 -0.12815521 -0.08345293
## DP_493_WW -0.13516116 -0.15994487 -0.12796214 -0.08092748
## FELISTANA_UA_7_18_WW -0.16710494 -0.15505734 -0.16452227 -0.22418501
## FM_958_WW -0.14219954 -0.15055165 -0.14715856 -0.15501596
## FUNTUA_FT_5_WW -0.11269389 -0.14227979 -0.11642073 -0.14602944
## LOCKETT_BXL_WW -0.16448783 -0.15415798 -0.14808086 -0.18946217
## MEXICO_910_WW -0.17249238 -0.17672182 -0.16613649 -0.17039570
## PD_3_WW -0.16678342 -0.13214900 -0.13706611 -0.16266860
## PLAINS_WW -0.10779132 -0.10267797 -0.11258470 -0.12783990
## TAM_86III_26_WW -0.13113223 -0.13625756 -0.12195914 -0.12236246
## TAM_91C_34_WW -0.11311105 -0.10997171 -0.10668380 -0.06541696
## TAM_94WE_37S_WW -0.17659283 -0.15219712 -0.14615555 -0.13805612
## VIR_6615_MCU_5_WW -0.15289211 -0.13514620 -0.13914343 -0.16666136
## VIR_7065_ALLEN_333_WW -0.14952381 -0.16242015 -0.14639242 -0.13531214
## VIR_7094_Coker_310_WW -0.18592978 -0.16791524 -0.17522145 -0.21419137
## VIR_7153_D_10_WW -0.14194026 -0.13810273 -0.14754579 -0.18705299
## VIR_7223_WW -0.15849310 -0.14315256 -0.13323395 -0.12600372
## WESTERN_STORMPROOF_WW -0.11563519 -0.14561095 -0.15272037 -0.10623065
## MEmagenta MEpink MEpurple MEred
## AC_134_CB_4029_WL 0.2697870752 -0.15340909 0.03956180 -0.11777167
## CB_4012_KING_KARAJAZSY_WL 0.2180950918 -0.12161539 -0.02863280 -0.09485857
## COKER_310_WL 0.0739603543 -0.17864483 0.10093827 -0.18613719
## DP_393_WL 0.2159616206 -0.13919236 0.11721489 -0.09650048
## DP_493_WL 0.1649711383 -0.16411829 0.30496247 -0.15351044
## FELISTANA_UA_7_18_WL 0.2430677145 -0.16250090 0.49104622 -0.19272880
## FM_958_WL 0.2263833528 -0.12549983 0.05963866 -0.13629735
## FUNTUA_FT_5_WL 0.0504200873 -0.13506433 0.15097480 -0.16474922
## LOCKETT_BXL_WL 0.1982958160 -0.13747926 0.25435651 -0.12901688
## MEXICO_910_WL 0.2176536940 -0.12701966 -0.03255451 -0.08856540
## PD_3_WL 0.1143316954 -0.13904729 0.03567477 -0.13766201
## PLAINS_WL 0.0277213957 -0.17740391 0.20062019 -0.19347607
## TAM_86III_26_WL 0.1094142817 -0.14201492 0.10072318 -0.15619928
## TAM_91C_34_WL 0.0867997820 -0.17519464 0.07999770 -0.15126325
## TAM_94WE_37S_WL 0.1538058947 -0.11476400 0.19171106 -0.11033480
## VIR_6615_MCU_5_WL 0.1851333173 -0.08121916 0.08563940 -0.09035553
## VIR_7065_ALLEN_333_WL 0.1844224443 -0.15280991 0.05953484 -0.15968919
## VIR_7094_Coker_310_WL 0.0296818878 -0.18928895 0.20248815 -0.19332726
## VIR_7153_D_10_WL 0.1109473680 -0.01216635 0.06339077 -0.05283009
## VIR_7223_WL 0.1367546949 -0.15183164 0.18564941 -0.19477708
## WESTERN_STORMPROOF_WL 0.0008261905 -0.13249692 0.04361368 -0.16292494
## AC_134_CB_4029_WW -0.1522254210 0.14506845 -0.12293384 0.16117553
## CB_4012_KING_KARAJAZSY_WW -0.0773218760 0.01479836 -0.11029394 -0.03211783
## COKER_310_WW -0.1356413710 0.07501822 -0.13179223 0.15832707
## DP_393_WW -0.1449374028 0.18385980 -0.15137163 0.18881039
## DP_493_WW -0.1787606338 -0.08788108 -0.14128347 0.03346255
## FELISTANA_UA_7_18_WW -0.1672264930 0.26079136 -0.10410550 0.20809442
## FM_958_WW -0.1323346270 0.27271354 -0.15300164 0.26665789
## FUNTUA_FT_5_WW -0.1285890371 0.09669244 -0.11318373 0.06811116
## LOCKETT_BXL_WW -0.1443121861 0.24120991 -0.15652952 0.24588586
## MEXICO_910_WW -0.1671194035 0.18979563 -0.15538175 0.16616449
## PD_3_WW -0.1425756666 0.19797248 -0.12646719 0.07306327
## PLAINS_WW -0.1200652723 0.14268906 -0.07401794 0.04695757
## TAM_86III_26_WW -0.1292227604 0.22596591 -0.13395045 0.18599313
## TAM_91C_34_WW -0.1327950608 0.07267629 -0.07202190 0.07833789
## TAM_94WE_37S_WW -0.1515496426 0.19592377 -0.14484000 0.15455214
## VIR_6615_MCU_5_WW -0.1488921665 0.03766545 -0.15329623 0.10899441
## VIR_7065_ALLEN_333_WW -0.1664161653 0.13821886 -0.13396496 0.11081286
## VIR_7094_Coker_310_WW -0.1738697294 0.13539693 -0.14103580 0.24804720
## VIR_7153_D_10_WW -0.1473591591 0.21587018 -0.11886439 0.22047677
## VIR_7223_WW -0.1355971118 0.07637702 -0.12618040 0.06881646
## WESTERN_STORMPROOF_WW -0.1416237108 0.08195903 -0.14203295 0.20235230
## MEturquoise MEyellow
## AC_134_CB_4029_WL -0.15546357 0.1963382029
## CB_4012_KING_KARAJAZSY_WL -0.12297016 0.1233792604
## COKER_310_WL -0.17250545 0.1800721240
## DP_393_WL -0.16062166 0.1409589191
## DP_493_WL -0.17386487 0.1007881064
## FELISTANA_UA_7_18_WL -0.16806650 0.2529243227
## FM_958_WL -0.14100380 0.1286613969
## FUNTUA_FT_5_WL -0.11667055 0.0996947469
## LOCKETT_BXL_WL -0.15026732 0.1130748134
## MEXICO_910_WL -0.13109777 0.0546899805
## PD_3_WL -0.17085060 0.1281256272
## PLAINS_WL -0.16601375 0.2195633323
## TAM_86III_26_WL -0.13933611 0.1949283615
## TAM_91C_34_WL -0.16612913 0.1924535205
## TAM_94WE_37S_WL -0.13982648 0.1205915796
## VIR_6615_MCU_5_WL -0.13137579 0.0008181377
## VIR_7065_ALLEN_333_WL -0.14788526 0.2179810929
## VIR_7094_Coker_310_WL -0.17416102 0.1489549346
## VIR_7153_D_10_WL -0.07884790 0.0966769484
## VIR_7223_WL -0.16620344 0.2796077314
## WESTERN_STORMPROOF_WL -0.14259675 0.0715369074
## AC_134_CB_4029_WW 0.19476903 -0.1746750265
## CB_4012_KING_KARAJAZSY_WW 0.08630843 -0.0820038135
## COKER_310_WW 0.14262211 -0.1200965796
## DP_393_WW 0.08729978 -0.1711147276
## DP_493_WW 0.06590144 -0.1203377931
## FELISTANA_UA_7_18_WW 0.24719603 -0.1540143663
## FM_958_WW 0.18099040 -0.1599476114
## FUNTUA_FT_5_WW 0.21961996 -0.1035977429
## LOCKETT_BXL_WW 0.19198928 -0.1754920758
## MEXICO_910_WW 0.19038627 -0.1712303288
## PD_3_WW 0.17091394 -0.1486752470
## PLAINS_WW 0.11738699 -0.1177219215
## TAM_86III_26_WW 0.09682428 -0.1500792284
## TAM_91C_34_WW 0.03288363 -0.1197998422
## TAM_94WE_37S_WW 0.12405501 -0.1739178609
## VIR_6615_MCU_5_WW 0.18362005 -0.1252971909
## VIR_7065_ALLEN_333_WW 0.15604069 -0.1550109640
## VIR_7094_Coker_310_WW 0.20630257 -0.1770153730
## VIR_7153_D_10_WW 0.19826660 -0.1623828870
## VIR_7223_WW 0.10518185 -0.1556589588
## WESTERN_STORMPROOF_WW 0.11719956 -0.1437505074