SNPRelate
SNPRelate copied to clipboard
zhengxwen
File format of groups file for Admixture analysis
Please advise what is the proper format for the "groups" file as it required for the Admixture analysis? According to the HClustering analysis, I may have 1 to 2 trees. I have a total of 19 samples to build the input vcf file. A attempted to use the sample,id as list for the groups file, but it returned with an error message indicating there is a problem with the groups matrix.
Here is the error message... prop <- snpgdsAdmixProp(RV, groups=groups)
Error in solve.default(mat[-length(groups), ] - matrix(T.P, nrow = length(T.P), : 'a' (20 x 1) must be square In addition: Warning message: In mat[-length(groups), ] - matrix(T.P, nrow = length(T.P), ncol = length(T.P), : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead.
str(groups) List of 21 $ A: chr "37" $ B: chr "38" $ C: chr "39" $ D: chr "40" $ E: chr "41" $ F: chr "42" $ G: chr "43" $ H: chr "44" $ I: chr "45" $ J: chr "46" $ K: chr "47" $ L: chr "48" $ M: chr "49" $ P: chr "51" $ Q: chr "52" $ R: chr "53" $ S: chr "54" $ T: chr "55" $ V: chr "57" $ N: chr "50" $ O: chr "56"
It seems that there are too many groups in the variable groups.
If you have three ancestral populations, you only need A, B and C in the variable groups.