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How to interate over folder and use as input for program running in Rstudio.

Hello, I'm in need of assistance in writing a small R-script.

I am using the program EditR, which is able to detect base editing from sanger sequence files. However, the tool only allows sequences to be uploaded one by one. Since I need to analyze a vast amount of sequences, I'd like to be able to upload in batch and write the output to one (or multiple) files.

The program is available in browser (https://moriaritylab.shinyapps.io/editr_v10/, as well as in Rstudio (https://github.com/MoriarityLab/EditR). (Haven't received any response from them) I am aware of the BEAT program (https://hanlab.cc/beat/) which is able to batch upload, although this is not performing as well for my application.

Since the Rstudio version of EditR is working without an internet connection, I was told that it is running "front end" and thus should be able to make alterations as to allow for batch uploading. But with my limited coding knowledge, I was unsuccessful in this. Could somebody help me on my way?

Kind regards, Bram

base-editing r sanger-sequencing editr batch-input
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updated by Hamid Ghaedi Hamid Ghaedi • written by Bram • Bram

I am not familiar with this tool, but if you want to run a tool over multiple files and write output to a file, here is a general idea:

res_list = c() # a list object to save results
for(i in 1:total_number_of_files)){
    obj = read_the_file_by_the_tool
    obj_proc = process_file_as_needed
    res_list[[i]] = obj_proc
}

You may get more detailed replies by showing what you have tried in R so far.

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written by Hamid Ghaedi Hamid Ghaedi

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