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raphaelmourad / DeepG4

DeepG4: A deep learning approach to predict active G-quadruplexes
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README: Example in 'Without accessibility' incomplete #1

Open HenrikBengtsson opened 3 years ago

HenrikBengtsson commented 3 years ago

FYI, the example under https://github.com/raphaelmourad/DeepG4#without-accessbility:

library(Biostrings)
library(DeepG4)

BED <- system.file("extdata", "test_G4_data.bed", package = "DeepG4")
BED <- import.bed(BED)

predictions <- DeepG4(X=sequences)
head(predictions)

doesn't work. For example, rtracklayer needs to be attached, and sequences is undefined.

HenrikBengtsson commented 3 years ago

I noticed that also several other example code snippets lacks library(rtracklayer).

rochevin commented 3 years ago

Thanks for pointing that out, rtracklayer is defined on the top on the README so it work when i run everything, but not when you run only parts. sequences is now defined too.

HenrikBengtsson commented 3 years ago

Thx. Yeah, I figured that out, but I can imagine a reader would expect those code snippets to be standalone, especially since library(...) is used at the top, which often indicates "script/code/example begins here".