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Directory provided does not exist

Hello, I don't have problem in reading single sample by the script:

GSM4837523.data <- Read10X(data.dir = "GSM4837523_02dat20190515tisCARconDIS_featurebcmatrixfiltered\\outs\\filtered_feature_bc_matrix")

But when I use the script to read all samples, I encounter the error: Directory provided does not exist.

dirs <- dir("C:\\Users\\nuora\\OneDrive\\Desktop\\GSE159677", full.names = TRUE)
length(dirs)

SRRs <- lapply(dirs, function(dir){
  CreateSeuratObject(counts = Read10X(paste(dir,"GSM4837523_02dat20190515tisCARconDIS_featurebcmatrixfiltered\\outs\\filtered_feature_bc_matrix", sep="/")), project = dir, min.cells = 3, min.features = 200)
})
read10x
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updated by Bastien Hervé Bastien Hervé • written by nuorain • nuorain

You are on windows, don't sep="/", use sep="\\"

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written by Bastien Hervé Bastien Hervé

Hi Bastien Herve, Thank you for your message. I got the same error.

Error in Read10X(paste(dir, "GSM4837523_02dat20190515tisCARconDIS_featurebcmatrixfiltered\\outs\\filtered_feature_bc_matrix",  : 
  Directory provided does not exist
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updated by Bastien Hervé Bastien Hervé • written by nuorain • nuorain

1 answer

Please consider being acquainted with basic level debugging. If the computer tells you that it cannot find the directory, make sure that the directory exist on your computer, or that the path to that directory is correct.

Put a print in your lapply and check if the directories exist.

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written by Bastien Hervé Bastien Hervé

Thanks. I deleted the extra file under the directory. Now it works. Have a nice day!!!

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written by nuorain • nuorain

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