Question: r-squared calculation && GAP package error
gravatar for Mk
2.0 years ago by
Germany, Berlin
Mk10 wrote:

I have 2 questions;

  1. I am trying to plot a regional association plot using the asplot function in gap package. The function requires a dataset similar to this one - Sample dataset. My question is how to calculate the r squared values from SNP ID's, It would be great if someone could give me some insights. I know LocusZoom is a easier alternative but I would like to do it in R.

  2. I was trying out the asplot function in gap package with sample data . I was following the steps detailed for creating the plot in the asplot function. I encountered an error in the following line,

    pos <- apply($SNP),1,GetSNPPosHapmap)

As far as my understanding the "GetSNPPosHapMap" function is sourced from "NCBI2R" package (which is now archived). When I run this line I get the following error;

Error in while (i <= nchar(within_text) & answer == (-1)) { : argument is of length zero

Can anyone suggest a solution for this?

Thanks in advance!!

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