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Read CytoSPACER Input Files

Source: R/data_io.R
read_cytospace_input.Rd

Read various input file formats supported by CytoSPACER.

Usage

read_cytospace_input(file_path, as_sparse = FALSE)

Arguments

file_path

Path to the input file. Supported formats:

  • .csv - Comma-separated values

  • .txt, .tsv - Tab-separated values

  • .mtx, .mtx.gz - Matrix Market format (sparse)

as_sparse

Logical. If TRUE, return sparse matrix. Default is FALSE.

Value

A data.frame or dgCMatrix (if sparse) with genes as rows and cells/spots as columns.

Details

For sparse matrix files (.mtx), the function expects companion files:

  • genes.tsv or features.tsv - Gene names

  • barcodes.tsv or cells.tsv - Cell/spot barcodes

Examples

if (FALSE) { # \dontrun{
expr <- read_cytospace_input("scRNA_data.csv")
expr_sparse <- read_cytospace_input("matrix.mtx", as_sparse = TRUE)
} # }