rJava in R Studio

This is just a note to myself rather than other.

I got a mail from my Boss asking if I could convert a table of markers/locus on the genome to an idiogram. That should be easy!, I thought.

As always I use bottom-up approach.

1. I found an R package plotting idiograms (karyoploteR).

2. To install it, I needed R 3.4. I had been running R.3.3 but latest version of R-studio. So I downloaded and updated R(not R studio) and restarted R. That helped me install KaryoploteR.

3. I converted the markers to chromosomal positions (in bp) and combined to make an excel file.

4. Now, I was not able to open ‘xlsx’ package in my R-studio. To finish the job I just used ‘readxl’ but many of my packages were using ‘xlsx’ package, so I had to get it working.

5. Although I solved by following the error messages, rather than answers
I had something like this problem. Link

#25 solved it.


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