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smcclatchy / mapping

Quantitative Trait Mapping Lesson
https://smcclatchy.github.io/mapping/
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Introduction comments: #2

Closed ytakemon closed 6 years ago

ytakemon commented 6 years ago
  1. Sample datasets: read_cross step is redundant from previous set up page. I think the two steps should be collapsed so you don't end up doing the same thing in 5 different steps, which seems to be the easiest way to confuse people (ie me :) ). 
    
# Redudant:
grav2 <- read_cross2( system.file("extdata", "grav2.zip", package="qtl2geno") )
grav2 <- read_cross2("http://kbroman.org/qtl2/assets/sampledata/grav2/grav2.zip")
grav2 <- read_cross2("~/my_data/grav2.zip")
zip_datafiles("~/my_data/grav2.yaml")
grav2 <- read_cross2("~/my_data/grav2.yaml")

From all these I think the easiest method is:

grav2 <- read_cross2( system.file("extdata", "grav2.zip", package="qtl2geno") )

but it would be good for everyone to download the sample data into their own directory

and learn to load data from their own machines:

grav2 <- read_cross2("~/my_data/grav2.yaml")

smcclatchy commented 6 years ago

Thanks for this, too, Yuka. I got rid of this entirely because it doesn't really meet learning goals - rather, it gets in the way.

Sue

ytakemon commented 6 years ago

I just took another look, and it looks great! I've never seen a visual workflow for qtl anlalysis, and I think it'll help with the mental conceptualization of the workshop. Where was this when I was learning this?!