6 months ago by
how can I use rtracklayer and liftover function to liftover from
Macaca Fascicularis genome to hg_19?
Even though this file exists, may I question to which extent it makes sense to lift-over between two different primate species? This certainly depends on your study and the scientific question, but it might mean that many loci will simply be dropped.
How can I convert them to genome positions?
First your example used human SNPs, therefore the outcome is not representative for the case where you use Macaque data.
You already have them. Your lifted data is in
cur19 after running your code.
This tells you that your data now is in a object of Class
gwaswloc which extends
?GRanges for a list of accessor methods to retrieve genomic coordinates.
Some of the most basic examples:
The data.frame call is used to export the content into a TSV file.