In need of help: Error in open.connection (file), opening tsv.gz & mtx.gz files

Trying to load the files and view the matrix as data table. This is what I have tried:

library(Matrix)
matrix_dir = "/Users/csb/Indexing/Exploratory data/data set/PIG/scRNA data/PBMC7_AllCells"
barcode.path <- paste0(matrix_dir, "barcodes.tsv.gz")
features.path <- paste0(matrix_dir, "features.tsv.gz")
matrix.path <- paste0(matrix_dir, "matrix.mtx.gz")
mat <- readMM(file = matrix.path)
feature.names = read.delim(features.path,
                           header = FALSE,
                           stringsAsFactors = FALSE)
barcode.names = read.delim(barcode.path,
                           header = FALSE,
                           stringsAsFactors = FALSE)
colnames(mat) = barcode.names$V1
rownames(mat) = feature.names$V1

But in stead i get this this error message:

Error in open.connection(file) : cannot open the connection
In addition: Warning message:
In open.connection(file) :
  cannot open file '/Users/csb/Indexing/Exploratory data/data set/PIG/scRNA data/PBMC7_AllCellsmatrix.mtx.gz': No such file or directory

Not sure where it went wrong, keeps failing when it tries to run at "mat <- readMM(file = matrix.path)"

dataframe python r studio

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updated 4.2 years ago by cpad0112

• written 4.2 years ago by Emily •

cannot open file '/Users/csb/Indexing/Exploratory data/data set/PIG/scRNA data/PBMC7_AllCellsmatrix.mtx.gz'

Please do not use spaces in directory/file names. If you replace the space with an _ this will work.

You could try escaping the spaces as /Users/csb/Indexing/Exploratory\ data/data\ set/PIG/scRNA\ data/PBMC7_AllCellsmatrix.mtx.gz but above option will be better.

• 0 views • link

written 4.2 years ago by GenoMax

you have a problem from these lines:

barcode.path <- paste0(matrix_dir, "barcodes.tsv.gz")
features.path <- paste0(matrix_dir, "features.tsv.gz")

Your directory path doesn't end with "/". When you do paste0 with directory and files, you will have an error like that (PBMC7_AllCellsmatrix.mtx.gz). Either you append / at the end of directory path or supply / in paste0 (/features.tsv.gz).

Btw, as GenoMax mentioned, do not use spaces or reserved characters in file paths and names.

• 0 views • link

written 4.2 years ago by cpad0112

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