R中主要成分(HCPC)层次聚类的P调整(FDR)

时间:2018-09-04 10:54:01

标签: cluster-analysis pca hierarchical false-positive

我现在正在使用“基于主成分的分层聚类(HCPC)”。分析结束时,HCPC函数将计算p值。 我进行了搜索,但找不到任何可以根据FDR和HCPC调整p值的函数。避免多变量集中的任何垃圾数据确实很重要。因此,我的问题是如何与HCPC一起进行p值调整?

这就是我现在正在做的事情:

#install.packages(c("FactoMineR", "factoextra", "missMDA"))
library(ggplot2)
library(factoextra)
library(FactoMineR)
library(missMDA)

library(data.table)
MyData <- fread('https://drive.google.com/open? 
id=1y1YbIXtUssEBqmMSEbiQGcoV5j2Bz31k')
row.names(MyData) <- MyData$ID
MyData [1] <- NULL
Mydata_frame <- data.frame(MyData)

# Compute PCA with ncp = 3 (Variate based on the cluster number)
Mydata_frame.pca <- PCA(Mydata_frame, ncp = 2, graph = FALSE)

# Compute hierarchical clustering on principal components
Mydata.hcpc <- HCPC(Mydata_frame.pca, graph = FALSE)

Mydata.hcpc$desc.var$quanti
                                                  v.test Mean in category  
Overall mean sd in category Overall sd      p.value
CD8RAnegDRpos                                  12.965378     -0.059993483 
-0.3760962775     0.46726224 0.53192037 1.922798e-38
TregRAnegDRpos                                 12.892725      0.489753272  
0.1381306362     0.46877083 0.59502553 4.946490e-38
mTregCCR6pos197neg195neg                       12.829277      1.107851623  
0.6495813704     0.48972987 0.77933283 1.124088e-37
CD8posCCR6neg183neg194neg                      12.667318      1.741757598  
1.1735140264     0.45260338 0.97870842 8.972977e-37
mTregCCR6neg197neg195neg                       12.109074      1.044905184  
0.6408258230     0.51417779 0.72804665 9.455537e-34
CD8CD8posCD4neg                                11.306215      0.724115486  
0.4320918842     0.49823677 0.56351333 1.222504e-29
CD8posCCR6pos183pos194neg                      11.226390     -0.239967805 
-0.4982954123     0.49454619 0.50203520 3.025904e-29
TconvRAnegDRpos                                11.011114     -0.296585038 
-0.5279707475     0.44863446 0.45846770 3.378002e-28

0 个答案:

没有答案