R语言学习小记之SCENIC

需要注意的是，nCores=10 在部分电脑上面不适用哦，主要是没办法开启并行计算。

报错：

Using 10 cores.
Warning in .AUCell_calcAUC(geneSets = geneSets, rankings = rankings, nCores = nCores,  :
  Using only the first 58.99 genes (aucMaxRank) to calculate the AUC.
Error in .AUCell_calcAUC(geneSets = geneSets, rankings = rankings, nCores = nCores,  : 
  Valid 'mctype': 'snow' or 'doMC'

解决：

修改代码为 nCores=1 即可 

scenicOptions <- initializeScenic(org = "hgnc", dbDir = "cisTarget_databases", nCores = 1)

此外

In runGenie3(as.matrix(exprMat.filtered.log), scenicOptions) :
  Only 498 (27%) of the 1839 TFs in the database were found in the dataset. Do they use the same gene IDs?

属于转录因子的居然有498个基因