Help with Setting up Pedigree Data

Hi all- I want to use R for some genetic computing. Specifically, I want to use this the Rare Variant Sharing Package (The RVS (Rare Variant Sharing) Package). However, I'm very new to R, and I'm not even sure how to load a pedigree, and all of the data into the R program. To clarify, what I"m trying to do, is to input a list of rare variant genes, and use this program to obtain the probability that these rare variant genes are associated with the phenotype shown in pedigrees which I have. How do I get started with inputting this type of data (both the gene lists and the pedigrees) into R?

Hi, here is an example of your own genome analysis, to get an idea on how to use R for genetics:

Thanks- I've been able to create a pedigree but am uncertain as to how I can insert the sequencing data for the members of the pedigree. Any ideas on how I would insert the sequencing data?

Hi, I found the RVS package manual: but I don't think pedigrees can be created. You can only use existing ones via data(samplePedigrees) . If you want to create pedigree you should use other packages ... If you google "create pedigree r" you will find many solutions.

Do you think that if I create the pedigree through another package, I can then use RVS accordingly? I'm trying to use the algorithm that allows for p value determination within a pedigree, and the algorithm that RVS employs would be perfect... if there's any advice on how to possibly incorporate my own input into RVS, that'd be great. Thanks so much

I would do this: in the pdf manual I linked to you I saw that the pedigree objects required by RVS are of type s3, so google "pedigree r s3" and find an r package that allows you to create a pedigree object and then try it with RVS.

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.