I'm using LDpred2 incorporated in bigsnpr to calculate polygenic scores with my own set of genetic Data. I am following the steps found in the online tutorial of LDpred2 on Github (https://privefl.github.io/bigsnpr/articles/LDpred2.html) to use the automatic model snp_ldpred2_auto.
I cannot execute the line:
pred_auto <- big_prodMat(G, beta_auto, ind.row = ind.test, ind.col = df_beta[["_NUM_ID_"]])
I suspect this happens because the matrices are not fit for multiplication with each other since the number of columns in G (the FBM matrix) is not identical as the number of rows in beta_auto (a common matrix). I intend to filter out variants (SNPs) from G such that the number of variants in G equals the number of variants in beta_auto .
I have never worked before with matrices of class FBM.code256 and do not know how to achieve this subsetting. Guidance is much appreciated.