I have been trying to use the radmixture package with my own input PED data, resulting from simulations.
However, for some SNPs, there will be some missing data (0 in the PED file).
I noticed that the function generateG (and gg) removes any SNPs that contain any missing data. Is there a rationale behind this? As far as I know (but I could not find much on this), ADMIXTURE does not do this.
Unfortunately, in my dataset there are only few SNPs for which no individuals have missing data, which thus reduces the power of the analysis by a great extent.
I have been trying to use the radmixture package with my own input PED data, resulting from simulations. However, for some SNPs, there will be some missing data (0 in the PED file).
I noticed that the function generateG (and gg) removes any SNPs that contain any missing data. Is there a rationale behind this? As far as I know (but I could not find much on this), ADMIXTURE does not do this.
Unfortunately, in my dataset there are only few SNPs for which no individuals have missing data, which thus reduces the power of the analysis by a great extent.