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totajuliusd / topr

topr is a collection of plotting functions for visualizing and exploring genetic association results. Association results from multiple phenotypes can be viewed simultaneously, over the entire genome (Manhattan plot) or in the more detailed regional view.
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Non-human genomes. #22

Open Eugenia-L opened 1 year ago

Eugenia-L commented 1 year ago

Is it possible to work with a different genome species? Can I incorporate an alternative annotation file for plotting?

totajuliusd commented 1 year ago

Sorry to say that topr only works with the human genome at the moment and can only be annotated with human genome builds 38 or 37.

totajuliusd commented 1 year ago

HI again, just wanted to let you know that you can make Manhattan plots for other species than human in the most recent version of topr (v 1.1.10). To do this, you have to include the argument get_chr_lengths_from_data=T in your manhattan function call, e.g.:

manhattan(CD_UKBB, get_chr_lengths_from_data = T)

However, the inbuilt annotation is only for the human genome, but if you have a Gene or Gene_Symbol column in your input data, topr will use this information for plotting instead.

totajuliusd commented 9 months ago

Hi, you can now use topr (v.2.0.0) with any species if you provide the gene annotation file as described here: https://github.com/totajuliusd/topr?tab=readme-ov-file#how-to-use-topr-with-other-species-than-human

AHinsu commented 4 months ago

Hi, I am trying the package with non-human species. The script to convert gtf to tsv works good. I realised that the script will only consider genes which have the geneSymbol and ignore others. My understanding is that there are many gene which don't have symbol and are referred by their Ensembl IDs, but they are protein-coding without proper annotation. So, just wondering if it should be alright to remove all the genes without geneSymbol or can you change the script to consider Ensembl ID if the geneSymbol is missing.

Thanks, Ankit