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gevaertlab / AMARETTO

Regulatory network inference and driver gene evaluation using integrative multi-omics analysis and penalized regression
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Preprocess error #11

Open kokyriakidis opened 5 years ago

kokyriakidis commented 5 years ago

Hello, I followed the R example but when I entered ProcessedData <- AMARETTO_Preprocess(DataSetDirectories) an error occurred:

Batch correction.
Error in TCGA_BatchCorrection_MolecularData(MA_TCGA, BatchData, MinPerBatch) : 
  argument "BatchData" is missing, with no default

any ideas?

jayendrashinde91 commented 5 years ago

Hi! Thanks for reaching out. We have fixed the issue you mentioned and have pushed the latest update. Running the following code should solve it for you now: ProcessedData <- AMARETTO_Preprocess(DataSetDirectories,BatchData) Best, Jay

kokyriakidis commented 5 years ago

Hi, now it says: 

Adjusting the Data
Loading MethylMix data.
    Getting MethylMix methylation states.
Error in eval(parse(text = paste("MET_TCGA=MethylStates$", CancerSite,  : 
  object 'MethylStates' not found

I specified as CancerSite LIHC

jayendrashinde91 commented 5 years ago

Hi, https://github.com/gevaertlab/AMARETTO/blob/ec2dddc21fb12fe39058cbe767376dd14672dcb3/AMARETTO_EXAMPLE/AMARETTO.R#L33 You need to load the MethylStates object to go ahead. We are constantly working on updating the package currently. And also a revised vignette will also be up for you to follow the package functions in a few days. Thanks

kokyriakidis commented 5 years ago

The R example says:

#ProcessedData <- AMARETTO_Preprocess(DataSetDirectories,BatchData)

#load(inst/extdata//MethylStates.rda) #MethylMix preprocessed data for CancerSite
#ProcessedData[[3]] <- MethylStates[CancerSite] #MethylMix preprocessed data for CancerSite

#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
# Loading preprocessed TCGA-LAML example dataset:
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
data("ProcessedDataLIHC")

#-----------------------------------------------------------------------------------------
# 4. Running AMARETTO
#-----------------------------------------------------------------------------------------
AMARETTOinit <- AMARETTO_Initialize(ProcessedDataLIHC,NrModules = 2, VarPercentage = 60)

1) So I load Methylstates first. Do I use this file for any kind of CancerSite?

2) Next, do I run ProcessedData <- AMARETTO_Preprocess(DataSetDirectories,BatchData) or something else from above?

3) What do I do next? ProcessedData[[3]] <- MethylStates[CancerSite] and then data("ProcessedDataLIHC")?

4) Then i run AMARETTOinit <- AMARETTO_Initialize(ProcessedDataLIHC,NrModules = 2, VarPercentage = 60) as it is? or I change ProcessedDataLIHC?