Error in running WGCNA

net = blockwiseModules(datExpr, power = softPower,
TOMType = "unsigned", minModuleSize = 30,
reassignThreshold = 0, mergeCutHeight = 0.25,
numericLabels = TRUE, pamRespectsDendro = FALSE,
saveTOMs = TRUE,
saveTOMFileBase = "BCell_TOM",
verbose = 3)

Calculating module eigengenes block-wise from all genes Flagging genes and samples with too many missing values... ..step 1 ....pre-clustering genes to determine blocks.. Projective K-means: ..k-means clustering.. ..merging smaller clusters... Block sizes: gBlocks 1 2 3 4947 3284 3053 ..Working on block 1 . TOM calculation: adjacency.. ..will use 11 parallel threads. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done. ..saving TOM for block 1 into file BCell_TOM-block.1.RData ....clustering.. ....detecting modules.. ....calculating module eigengenes.. ....checking kME in modules.. ..removing 326 genes from module 1 because their KME is too low. ..removing 226 genes from module 2 because their KME is too low. ..removing 3 genes from module 4 because their KME is too low. ..removing 4 genes from module 5 because their KME is too low. ..Working on block 2 . TOM calculation: adjacency.. ..will use 11 parallel threads. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done. ..saving TOM for block 2 into file BCell_TOM-block.2.RData ....clustering.. ....detecting modules.. ....calculating module eigengenes.. ....checking kME in modules.. ..removing 198 genes from module 1 because their KME is too low. ..removing 25 genes from module 2 because their KME is too low. ..removing 32 genes from module 3 because their KME is too low. ..removing 7 genes from module 4 because their KME is too low. ..removing 1 genes from module 5 because their KME is too low. ..removing 6 genes from module 6 because their KME is too low. ..removing 6 genes from module 7 because their KME is too low. ..removing 11 genes from module 9 because their KME is too low. ..removing 6 genes from module 10 because their KME is too low. ..removing 1 genes from module 17 because their KME is too low. ..Working on block 3 . TOM calculation: adjacency.. ..will use 11 parallel threads. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done. ..saving TOM for block 3 into file BCell_TOM-block.3.RData ....clustering.. ....detecting modules.. ....calculating module eigengenes.. ....checking kME in modules.. ..removing 143 genes from module 1 because their KME is too low. ..removing 33 genes from module 2 because their KME is too low. ..removing 48 genes from module 3 because their KME is too low. ..removing 44 genes from module 4 because their KME is too low. ..removing 22 genes from module 5 because their KME is too low. ..removing 18 genes from module 6 because their KME is too low. ..removing 2 genes from module 7 because their KME is too low. ..removing 2 genes from module 9 because their KME is too low.
Error in (new("standardGeneric", .Data = function (x, y = NULL, use = "everything", : unused arguments (weights.x = NULL, weights.y = NULL, cosine = FALSE) Traceback:

blockwiseModules(datExpr, power = softPower, TOMType = "unsigned", . minModuleSize = 30, reassignThreshold = 0, mergeCutHeight = 0.25, . numericLabels = TRUE, pamRespectsDendro = FALSE, saveTOMs = TRUE, . saveTOMFileBase = "SLE_BCell_TOM", verbose = 3)

do.call(match.fun(corFnc), c(list(datExpr[, goodLabels != 0], . AllMEs), if (corFncAcceptsWeights) list(weights.x = if (haveWeights) weights[, . goodLabels != 0] else NULL, weights.y = NULL) else NULL, . corOptions))

# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # biostas 퀴즈판 게시물에서 고수가 해답을 했다. # Error in (function...)thrown by WGCNA tutorial (R)
이유는 WGCNA와 다른 소프트웨어 패키지 간의 충돌입니다.WGCNA의 cor 함수와 R에 있는 cor는 이름 공간에서 충돌합니다.해결 방법은 이 함수를 사용하기 전에 잠시 기능을 재분배하는 것입니다. 아래의 정확한 사용법 cor net = blockwise Modules(datExpr, power = 6, TOM Type ='unsigned', minModule Size = 30,reassign Threshold = 0, merge CutHeight = 0.25,numeric Labels = TRUE,pam Respects Dendro = FALSE,saveTOMs = TRUE,savetom File Base ='female Mouse TOM','verbose = 3) cor
As correctly answered by multiple people here, the problem is that WGCNA has its own function "cor"and this correlates in the namespace with "cor"from the package stats.
Rather than loading and unloading modules or restarting R one might as well temporarily re-assign the function: