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Table 3 Correlations between predicted and observed body mass index for all genotype masking rates and family layouts

From: Effect of genotype imputation on genome-enabled prediction of complex traits: an empirical study with mice data

90% genotype masking rate

Model*

Across families

Within families

1809

1809ia

201

1809

1809ia

201

BL

0.227

0.193

0.191

0.199

0.164

−0.047

RKHS

0.238

0.195

0.199

0.208

0.132

−0.054

BRANN

0.112

0.092

0.147

0.163

0.041

0.054

75% genotype masking rate

Model*

Across families

Within families

1809

1809ib

453

1809

1809ib

453

BL

0.228

0.219

0.199

0.200

0.196

0.184

RKHS

0.238

0.226

0.211

0.208

0.204

0.200

BRANN

0.118

0.115

0.145

0.172

0.154

0.170

50% genotype masking rate

Model*

Across families

Within families

1809

1809ic

905

1809

1809ic

905

BL

0.227

0.231

0.225

0.199

0.197

0.189

RKHS

0.238

0.238

0.236

0.207

0.206

0.202

BRANN

0.118

0.131

0.149

0.172

0.168

0.149

  1. aImputed from 201 SNPs.
  2. bImputed from 453 SNPs.
  3. cImputed from 905 SNPs.
  4. *BL: Bayesian LASSO; RKHS: Reproducing Kernel Hilbert Spaces (RKHS) and; BRANN: Bayesian Regularized Neural Networks.