The shiny app version of Fragman
I generate data that has a series of peaks, representing fragments of DNA, in 5 colored channels. The raw output has time on the x-axis and peak height (in rfu, or relative fluorescence units) on the y axis
One channel contains a reference (known as a ladder). This has DNA fragments of known size. Using this reference, you can convert the x-axis from time to base-pair units.
I currently use the fragman program to 'call' the ladder peaks. Sometimes some peaks are missing (because of bleed-through from other channels), so often you need to manually correct the ladder calls.
I'd like to create a shiny-based web app to do what fragman does. It needs to display the data from one file at a time, display the calls it automatically assigns, and allow the user to remove bad calls (e.g. by right click) and add correct calls (e.g. by left click).
I will then integrate this into my analysis pipeline, which will also be shiny app-based.
I've written a manual script that does what I want it to, which can be used as a reference. However, I need help making this shiny compatible.
The bit I'm having trouble with is up to '[login to view URL](d, file = "./data/[login to view URL]", [login to view URL] = FALSE)'
But if you can streamline the whole workflow and get it on shiny I'd be happy.
It's got the data in there in /fsa.
I've got lots of other demo files (gigabytes).
I attached my codes and example data.
50, 75, 100, 125, 150, 200, 250, 300, 350, 400, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950 and 1000 base pairs ([login to view URL]~0495fed3-7a77-41f4-9d32-87b93c4bbeba)
The ladder in these ones is in channel_4. It's got the same DNA fragments in though, just with a different dye.
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