We have an RAPD genetic data with the usage of 8 loci/primer, for each loci there is about 13-18 "allels". My problem is that I am stucked at the beginning. I dont know how shall I need to prepare the import file, to be sure that each alleles will connected to their own loci.
RAPDs are dominant markers (presence/absence). It is impossible to have 13-18 alleles for a dominant marker.
I think that you may mean that you used 8 primers and that each produced 13-18 polymorphic fragments (bands). If that is the case, then each combination of band and primer is a single locus. Your data set should be a table ("data frame" in R) where each individual is a row and each locus is a column. The presence or absence of the fragment at a given locus for a given individual should be indicated by a 1 (presence), a 0 (absence), or a NA (for individuals with no amplification with that primer).
Pg. 17 of the vignette that I have linked to below (section 4.3) describes how to handle presence/absence data in adgenet. As it states, the package is designed for codominant marker data, so some functionality will be unavailable to you. There may be other packages better suited to the analysis of your data. Maybe some others will have suggestions for you regarding this.
Best of luck with your research!
http://adegenet.r-forge.r-project.org/files/tutorial-basics.pdf
Dear Jack,
Yes, I was wrong, I meant fragment. Thank you so much for your help. I will try it. :)
Best regards,
David
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology