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edcarp / genomics-r-intro

Intro to R and RStudio for Genomics, University of Edinburgh
https://edcarp.github.io/genomics-r-intro/
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Decide which R read[._]csv function to use #5

Open baileythegreen opened 3 years ago

baileythegreen commented 3 years ago

All the data for the R for genomics workshop is on a figshare instance with nice instructions. https://figshare.com/articles/Data_Carpentry_Genomics_beta_2_0/7726454

From that we only need combined_tidy_vcf.csv, for episode 3, factors and data frames onwards. I can download that with either

variants <- read.csv("https://ndownloader.figshare.com/files/14632895",stringsAsFactors = FALSE)
variants <- readr::read_csv("https://ndownloader.figshare.com/files/14632895")

So for the material we are starting with, we don't need to have a separate git repo.

@FlicAnderson let's decide if we want to use base R read.csv or tidyverse read_csv - better, but requires updating lesson materials before Wednesday.

FlicAnderson commented 3 years ago

@baileythegreen I think using readr::read_csv() makes most sense to me, let's go with that

baileythegreen commented 3 years ago

@FlicAnderson

I was just capturing things from the Slack discussion on Saturday here so they didn't get lost. No need to run instructional decisions by me.

ewallace commented 3 years ago

Related to datacarpentry/genomics-r-intro#85.

That means that, if we find a nice read_csv solution here, we should PR it into the datacarpentry repository.