未找到 WGCNA 函数

Question

我正在按照本教程将 WGCNA 应用于 RNASeq 数据。 对于几个函数，它给我一个错误，即找不到包函数。

> sft <- pickSoftThreshold(normalized_counts,
+                          dataIsExpr = TRUE,
+                          corFnc = cor,
+                          networkType = "signed"
+ )
Error in pickSoftThreshold(normalized_counts, dataIsExpr = TRUE, corFnc = cor,  : 
  could not find function "pickSoftThreshold"

我试图确保包被正确调用，但是当我调用它时出现以下错误：

> library(WGCNA)
Error: package or namespace load failed for ‘WGCNA’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘xfun’
In addition: Warning message:
package ‘WGCNA’ was built under R version 4.1.3

所以我尝试安装包“xfun”：

> install.packages("xfun")
Installing package into ‘C:/Users/me/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/xfun_0.31.zip'
Content type 'application/zip' length 401092 bytes (391 KB)
downloaded 391 KB

package ‘xfun’ successfully unpacked and MD5 sums checked
Error in install.packages : ERROR: failed to lock directory ‘C:\Users\me\Documents\R\win-library\4.1’ for modifying
Try removing ‘C:\Users\me\Documents\R\win-library\4.1/00LOCK’

我关注了一些建议尝试以下代码来解决错误的线程：

> install.packages("xfun", dependencies = TRUE, INSTALL_opts = '--no-lock')
package ‘pkgbuild’ successfully unpacked and MD5 sums checked
Error in install.packages : ERROR: failed to lock directory ‘C:\Users\parnian\Documents\R\win-library\4.1’ for modifying
Try removing ‘C:\Users\me\Documents\R\win-library\4.1/00LOCK’

我不知道如何克服这些错误才能使用诸如pickSoftThreshold() 之类的WGCNA 函数。 你能帮助我吗？

Answer 1

转到您的库文件夹： C:\Users\me\Documents\R\win-library\4.1/并删除所有以00LOCK开头的文件夹

重启 R 然后尝试重新安装xfun和WGCNA