Hi,
I am trying to make a Manhattan plot using R ggplot following the example here (https://www.r-graph-gallery.com/101_Manhattan_plot.html).
I am using our own data produced from a GWAS and our results are in csv files; together, 23 csv files with each chromosome result in one csv file. Because these are summary statistics without personal identifiers, I have downloaded each cvs file and was planned to load them into R and then proceed with ggplot.
The problem is, each cvs file is huge, ~1.5 G each, so it's taking my computer a really long time to load just one single file. Any suggestions? I do have access to our university server but it's Unix-command based and I don't think I can run R interactively there.
It's likely that R is installed on your university's cluster and that you can run it there (check using "module avail R"). I would just read the data, create your plot, save it to a png, and then scp it back to your local machine. Note: There are many different ways to read large csv files in R -- some much faster than others (see here for more details). I hope this helps!
Oh wow, vroom is A LOT faster. Thank you, Chris!