Skip to main content

Table 5 Prediction mean squared errors for body mass index analysis by family layouts and genotype masking rates

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

0.002

0.002

0.002

0.002

0.002

0.002

RKHS

0.002

0.002

0.002

0.002

0.002

0.002

BRANN

0.013

0.014

0.010

0.042

0.036

0.024

75% genotype masking rate

Model*

Across families

Within families

1809

1809ib

453

1809

1809ib

453

BL

0.002

0.002

0.002

0.002

0.002

0.002

RKHS

0.002

0.002

0.002

0.002

0.002

0.002

BRANN

0.021

0.023

0.015

0.044

0.045

0.041

50% genotype masking rate

Model*

Across families

Within families

1809

1809ic

905

1809

1809ic

905

BL

0.002

0.002

0.002

0.002

0.002

0.002

RKHS

0.002

0.002

0.002

0.002

0.002

0.002

BRANN

0.021

0.023

0.016

0.040

0.040

0.047

  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.