Load cvs files into R to make manhattan plots using ggplot

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2.1 years ago

a304ced8 ▴ 10

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.

r ggplot plot manhatton • 948 views

ADD COMMENT • link 2.1 years ago by a304ced8 ▴ 10

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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!