I'm running into an issue with sporadic missingness when using admixmmap function from Genesis.
Column `rsids` joining factor and character vector, coercing into character vector Reading in Phenotype and Covariate Data... Fitting Model with 7485 Samples Computing Variance Component Estimates using AIREML Procedure... Sigma^2_A Sigma^2_E logLik RSS Running analysis with 7485 Samples and 43221 SNPs Beginning Calculations... Block 1 of 9 Completed - 1.645 mins Block 2 of 9 Completed - 1.128 mins Block 3 of 9 Completed - 38.08 secs Block 4 of 9 Completed - 47.14 secs Block 5 of 9 Completed - 42.99 secs Block 6 of 9 Completed - 1.203 mins Error in prepareGenotype(genoData = admixDataList[[i]], snp.read.idx = snp.include$index[bidx], : genoData has sporadic missingness in block size > 1 Calls: admixMapMM -> prepareGenotype Execution halted
I'm left with one chromosome to wrap up the analysis.
Is it possible to identify region the function is giving issues for missingness? Is it due to large number of SNPs, or low number of SNPs, or high linkage equilibrium?
SNPRelate_1.12.2 argparse_2.0.1 GENESIS_2.8.1 dplyr_0.8.0.1 gdsfmt_1.14.1 GWASTools_1.24.1 Biobase_2.38.0 BiocGenerics_0.24.0 R version 3.4.2 (2017-09-28)
Thanking you in advance.