Signed networks.The choice of signed vs. unsigned networks is complex, but in general we prefer signed (or "signed hybrid") networks to unsigned networks. To construct signed networks, use argumenttype = "signed"ortype = "signed hybrid"in functions such asaccuracyMeasures, adjacency, chooseOneH...
1)unsigned: 2)signed: 第一种情况,认为具有高负相关的gene之间,是有联系的。 第二种情况,认为具有高负相关的gene之间,是没有联系的。 举个例子, 假设cor = -1,β=2,unsigned情况下,计算得到的adjacency为1,即gene之间高度关联。signed情况下,计算得到的adjacency为0,即gene之间无关联。 3)TOM矩阵的构建 引...
if (is.na(power)){ power = ifelse(nSamples<20, ifelse(type == 'unsigned', 9, 18), ifelse(nSamples<30, ifelse(type == 'unsigned', 8, 16), ifelse(nSamples<40, ifelse(type == 'unsigned', 7, 14), ifelse(type == 'unsigned', 6, 12)) ) )} 网络构建 ##一步法网络构建...
Chen CCold Spring Harbor LaboratoryR. Dai, Y. Xia, C. Liu, C. Chen, csuWGCNA: A combination of signed and unsigned WGCNA to capture negative correlations. bioRxiv 288225 [Preprint]. 27 September 2018. https://doi.org/10.1101/288225....
(可用boxplot查看基因表达分布是否一致),需要quantile normalization exprMat <- "LiverFemaleClean.txt" trait <- "TraitsClean.txt" # 官方推荐 "signed" 或 "signed hybrid" type = "unsigned" # 相关性计算 # 官方推荐 biweight mid-correlation & bicor # corType: pearson or bicor corType = "pearson...
networkType:计算邻接矩阵时,是否考虑正负相关性;默认为"unsigned",可选"signed", "signed hybrid" TOMType:计算TOM矩阵时,是否考虑正负相关性;默认为"signed",可选"unsigned"。但是根据幂律转换的邻接矩阵(权重)的非负性,所以认为这里选择"signed"也没有太多的意义。
exprMat<-"WGCNA/LiverFemaleClean.txt"# 官方推荐"signed"或"signed hybrid"# 为与原文档一致,故未修改 type="unsigned"# 相关性计算 # 官方推荐 biweight mid-correlation&bicor # corType:pearson or bicor # 为与原文档一致,故未修改 corType="pearson"corFnc=ifelse(corType=="pearson",cor,bicor)# ...
2.2 强烈不建议采用差异表达的基因进行WGCNA分析， 因为差异表达的基因，就是的样本失去了多样性。3. ...
seurat_obj, networkType = 'signed' # you can also use "unsigned" or "signed hybrid" ) ...
# networkType:计算邻接矩阵时,是否考虑正负相关性;默认为"unsigned",可选"signed", "signed hybrid" # TOMType:计算TOM矩阵时,是否考虑正负相关性;默认为"signed",可选"unsigned"。但是根据幂律转换的邻接矩阵(权重)的非负性,所以认为这里选择"signed"也没有太多的意义。 # numericLabels: 返回数字而不是颜色...