[R] Help on MFAmix to Reduce Dimensions for a Genetic Dataset

[Xu, Bingze]

Dear R Help Members,


I am a student from Washington University in St. Louis and I am working on a genetic project in R. In this dataset, there are 497 rows and 11,226 columns. Every row is a genetic marker series for a particular hybrid, and every column is a genetic marker with value 1, 0, -1 and NA. I am trying to reduce the dimensions of this dataset because I want to combine this one and other weather datasets for further predictions.


However I encountered two problems after I read the package instructions carefully:

1, For groups and name.groups, I set them as seq(1, ncol(geno)) and colnames(geno) respectively, where geno is the variable name for test_fill. I have attached this dataset for your reference. I am wondering if these settings are correct.


2, Error: There are columns in X.quali where all the categories are identical keeps popping out. Since I do not know much about the genetic dataset and I do not want to remove the columns even if those two columns are identical, what can I do next?


Thank you very much and I look forward to your reply.

Best wishes,
Bingze Xu
Graduate Student - M.S. in Business Analytics
Washington University in St. Louis
Email: bingzexu using wustl.edu
Phone: +1 314-665-8323