hi
I use TCGA Assembler2 for data integration.
when run below codes this error occurred: Error in strsplit(TCGABarcode, split = "-") : non-character argument
how solve this error?
TNX
inputDataList <- vector("list", 5)
inputDataList[[1]] <- list(Des = GeneExpData$Des, Data = GeneExpData$Data, dataType = "geneExp")
inputDataList[[2]] <- list(Des = Methylation450_TSS1500_DHS$Des, Data = Methylation450_TSS1500_DHS$Data, dataType = "methylation")
inputDataList[[3]] <- list(Des = GeneLevelCNA$Des, Data = GeneLevelCNA$Data, dataType = "copyNumber")
inputDataList[[4]] <- list(Des = RPPAData$Des, Data = RPPAData$Data, dataType = "protein_RPPA")
inputDataList[[5]] <- list(Des = miRNASeqData$Des, Data = miRNASeqData$Data, dataType = "miRNAExp")
MergedData <- CombineMultiPlatformData(inputDataList = inputDataList)
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roohallah1435 •
We are passing some factors to strsplit, to reproduce:
strsplit("my-factor-text", split = "-")
# [[1]]
# [1] "my" "factor" "text"
strsplit(factor("my-factor-text"), split = "-")
# Error in strsplit(factor("my-factor-text"), split = "-") :
# non-character argument
I am guessing you are using the TCGA-Assembler-2 from GitHub. When creating the input object - inputDataList, your list contains factors, not character class.
yes. I am using the TCGA-Assembler-2 .
how solve this problem?
TNX in advance
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this is a TCGABarcode sample: TCGA-A6-3807-01A.22
Do not add an answer unless you're answering the top level question. I've moved this to a comment now, but use
Add CommentorAdd Replyat the appropriate spot in the future.class(TCGABarcode)?ATPoint is asking if the sample you provided above is a string in R or you just typed in the object name and it rendered a string representation of a more complex object.
class(xyz)shows what type of objectxyzis.Please understand the concept behind these clarifying questions, copy-pasting code verbatim never works.
From your error, it seems obvious that your environment when you ran the command in the question
strsplit(TCGABarcode, split = "-")is not the same as your environment now, as the objectTCGABarcodedefinitely existed in that environment while it doesn't exist now.I'm sorry I am very amateur and recently I work with R I'm confused now Now I am trying to solve the problem, if not resolved will come back again. thank you for your attention