cannot open file '/Users/seanwen/Documents/U2AF1_2019/Linker/rMATS/ASEvents/fromGTF.RI.txt': No such file or directory

[Cp0728]

df <- read.table(paste("D:\deskface\MARVEL\format_rmats\fromGTF.RI.txt", sep=""), sep="\t", header=TRUE, stringsAsFactors=FALSE)

Format BED file

RI_Coordinates.bed <- PrepareBedFile.RI(file=df)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '/Users/seanwen/Documents/U2AF1_2019/Linker/rMATS/ASEvents/fromGTF.RI.txt': No such file or directory

The above is my error, I used the example data to generate fromGTF.RI.txt, but the path is wrong when running, please ask if this is a bug

[Cp0728]

In this function Script_PLATE_00_rMATS_06_CreateBedFile_RI. R, you added an absolute path that caused the run to be called automatically, I hope you can change that

[Cp0728]

thanks

[kztz05]

Hi there,
You can solve this by modifying PrepareBedFile.RI function.
PrepareBedFile.RI is defined in R/Script_PLATE_00_rMATS_06_CreateBedFile_RI.R, first remove hard-coded path (below):

# Example arguments (DELETE THESE LINES)
path <- "/Users/seanwen/Documents/U2AF1_2019/Linker/rMATS/ASEvents/"
file <- "fromGTF.RI.txt"
df <- read.table(paste(path, file, sep=""), sep="\t", header=TRUE, stringsAsFactors=FALSE)

Then generalize the function:

PrepareBedFile.RI <- function(file) {
    # Handle input (file path or data frame)
    if (is.character(file)) {
        df <- read.table(file, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
    } else {
        df <- file
    }
    
    # Rest of the original code...
}

Last rebuild and install the package from source. (Remember to remove the original package)