| Class | Analysis and data manipulation command |
| Name | blup |
| Arguments | (<quantitative trait> <h2>) | (<autosomal marker> [<binary trait> | (<quantitative trait> [(>|>=|<|<=|==|^= <threshold>]))). |
Calculates BLUPs (best linear unbiased predictions of the breeding value) for a quantitative trait assuming the given heritability.
If a marker locus is specified, the BLUEs (best linear unbiased estimates) of the marker allele frequencies are calculated, following McPeek et al [2004]:
ai = (1' A-1 1)-1 1' A-1 zi ,
where,
A is the numerator relationship matrix
zi is a score representing the count for the ith allele in each
individual (0, 0.5, 1).
If a second binary or thresholded quantitative trait is also specified, the BLUEs for the marker allele frequencies for individuals matching the criterion is printed.
McPeek et al [2007] note that the BLUEs are occasionally negative.
Increasing the plevel to 1 gives the BLUE ASEs.
Example:
>> blu D14S52
------------------------------------------------
BLUE allele frequencies for locus "D14S52"
------------------------------------------------
Allele Frequency Count Histogram
57 0.0067 0 *
69 0.0461 2 *
81 0.0213 1 *
83 0.5020 21 **********
85 0.1514 6 ***
87 0.2177 9 ****
93 0.0550 2 *
Number of alleles = 7
Heterozygosity (Hu) = 0.6885
Poly. Inf. Content = 0.6308
4 Neff mu (SSMM) = 3.60518644
Number persons typed = 21 ( 27.3%)
>> fre D14S52
------------------------------------------------
Allele frequencies for locus "D14S52"
------------------------------------------------
Allele Frequency Count Histogram
57 0.0238 1 *
69 0.0238 1 *
81 0.0476 2 *
83 0.4286 18 *********
85 0.1905 8 ****
87 0.2381 10 *****
93 0.0476 2 *
Number of alleles = 7
Heterozygosity (Hu) = 0.7352
Poly. Inf. Content = 0.6763
4 Neff mu (SSMM) = 4.88968079
Number persons typed = 21 ( 27.3%)
>> mcf D14S52
------------------------------------------------
MCEM allele frequencies for locus "D14S52"
------------------------------------------------
Allele Frequency Count Histogram
57 0.0418 2 *
69 0.0432 2 *
81 0.0441 2 *
83 0.4944 19 **********
85 0.0854 3 **
87 0.2491 9 *****
93 0.0419 2 *
Number of alleles = 7
Heterozygosity (Hu) = 0.6972
Poly. Inf. Content = 0.6394
4 Neff mu (SSMM) = 3.67040887
Number of founders = 19 ( 2.6% typed)
#
# Compare to MLEs from MENDEL and BLUEs from MQLS
#
# Allele MLE (ASE) BLUE (SE)
# ------ --------------- ---------------
# 57 0.0431 (0.0422) 0.0067 (0.0185)
# 69 0.0431 (0.0422) 0.0461 (0.0476)
# 81 0.0431 (0.0422) 0.0213 (0.0328)
# 83 0.4950 (0.1072) 0.5020 (0.1136)
# 85 0.0822 (0.0639) 0.1514 (0.0814)
# 87 0.2505 (0.0915) 0.2177 (0.0938)
# 93 0.0431 (0.0422) 0.0550 (0.0518)
#
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