search

gevaertlab / AMARETTO

Regulatory network inference and driver gene evaluation using integrative multi-omics analysis and penalized regression
Apache License 2.0
16 stars 12 forks source link

AMARETTO Results #16

Open Srinathkandalam opened 3 years ago

Srinathkandalam commented 3 years ago

Hello

I tried run AMARETTO which was given in google collab for the already processed data and followed the same exact steps [https://colab.research.google.com/drive/1JfnRoNgTVX_7VEGAAmjGjwP_yX2tdDxs#scrollTo=1XemfQskXI2N].

I had the following error in the results section. Please help me out. RStudio 06-04-2021 22_22_32

Code: MA_matrix_LIHC = read_gct("https://datasets.genepattern.org/data/module_support_files/Amaretto/TCGA_LIHC_Expression.gct") CNV_matrix_LIHC = read_gct("https://datasets.genepattern.org/data/module_support_files/Amaretto/TCGA_LIHC_CNV.gct") MET_matrix_LIHC = read_gct("https://datasets.genepattern.org/data/module_support_files/Amaretto/TCGA_LIHC_Methylation.gct") ProcessedData_LIHC = list(MA_matrix=MA_matrix_LIHC, CNV_matrix=CNV_matrix_LIHC, MET_matrix=MET_matrix_LIHC) data("Driver_Genes") TF_candidate_drivers <- Driver_Genes$TFs_TFutils_union

combination_method <- "union" NrModules = 150 VarPercentage = 75 NrCores = 4 AMARETTOinit <- AMARETTO_Initialize(ProcessedData = ProcessedData_LIHC, Driver_list = TF_candidate_drivers, method = combination_method, NrModules = NrModules, VarPercentage = VarPercentage, NrCores = NrCores) AMARETTOresults <- AMARETTO_Run(AMARETTOinit = AMARETTOinit)

Error Found 734 CNV driver genes. Found 1816 MethylMix driver genes. Found 947 driver genes from the input list. Found a total of 3177 unique drivers with your selected method.

AMARETTOresults <- AMARETTO_Run(AMARETTOinit = AMARETTOinit) Running AMARETTO on 11180 genes and 367 samples. Stopping if less then 111.8 genes reassigned. Autoregulation is turned ON. Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent In addition: Warning message: In (function (..., deparse.level = 1) : number of rows of result is not a multiple of vector length (arg 1)