Error in strsplit(TCGABarcode, split = "-") : non-character argument

Question

[roohallah1435]

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)

[roohallah1435]

this is a TCGABarcode sample: TCGA-A6-3807-01A.22

[Ram]

Do not add an answer unless you're answering the top level question. I've moved this to a comment now, but use Add Comment or Add Reply at the appropriate spot in the future.

[ATpoint]

class(TCGABarcode) ?

[roohallah1435]

> class(TCGABarcode)

Error: object 'TCGABarcode' not found

[Ram]

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 object xyz is.

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 object TCGABarcode definitely existed in that environment while it doesn't exist now.

[roohallah1435]

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

Answer 1

[zx8754]

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.

[roohallah1435]

yes. I am using the TCGA-Assembler-2 .

how solve this problem?

TNX in advance

[Ram]

1. Use as.character() to convert an object from factor to character (string)
2. Please use professional language and avoid jargon such as "TNX". Use the proper "Thanks" instead.

Answer 2

[ATpoint]

TCGABarcode is not a split-able character and probably a list if I interpret this code at the bottom correctly. Can you show the content of this variable?

Splitting a list:

tmp <- as.list(c("hi-ho", "foo-bar"))
sapply(tmp, function(x) strsplit(x, split="-"))