Haseman Elston Regression - gc5k/GEAR GitHub Wiki
The Haseman-Elston regression for GWAS
It provides a procedure that estimates the additive variance components for GWAS data.
Citation:
Chen, G.B., Estimating heritability of complex traits from genome-wide association studies using IBS-based Haseman-Elston regression, 2015, Front Genet:5:107
Chen, G.B., On the reconciliation of missing heritability for genome-wide association studies, 2016, Euro J Hum Genet, 2016, 24:1810:6
Master command: he
There are three kinds of Haseman-Elston regressions implemented. The three options are
-
--sd: it models the phenotype as (y-y)2
-
--ss: it models the phenotype as (y+y)2
-
--cp: it models the phenotype as y*y
--grm
This option will read a pair of files: file.grm.gz, file.grm.id. The grm files can be generated with grm option.
--grm-list
This option provides a file which contains a list of grm file pairs. For example, if the file reads as:
file1
file2
...
fileN
then GEAR will search for pairs fileX.grm.gz and fileX.grm.id.
--grm-bin
This option provides a pair of files: file.grm.bin (binary format), file.grm.id. The grm binary files can be generated with GCTA.
--grm-bin-list
Analogous to grm-list, but in this case GEAR searches for fileX.grm.bin and fileX.grm.id.
--grm-cutoff
This option specifies the cut-off for grm. Any grm scores greater than the cutoff will be discarded.
Notes: neither grm-cutoff nor grm-abs-cutoff works for grm-list and grm-bin-list options.
--pheno
This option specifies the phenotype file, in which the first column is family IDs, the second column is individual IDs, and the rest are phenotype columns. Missing values were "-9", "NA", "na", "-Inf", and "Inf".
--mpheno
This option specifies the target trait or phenotype column that is used in Haseman-Elston regression. By default, mpheno=1, meaning the first phenotype column (i.e. the third column in the phenotype file).
--scale
This option will standardize the phenotype.
--keep
If specifies the individuals should be kept in the analysis.
--jackknife/--jk
Jackknife for evaluating the sampling variance for HE regression.
Examples
gear he --sd --grm test --pheno test.phe --out he-test --scale
gear he --sd --grm test --pheno test.phe --jk --out he-test --scale
gear he --sd --grm test --pheno test.phe --grm-cutoff 0.1 --out he-test
gear he --sd --grm test --scale --pheno test.phe --mpheno 1 --out he-test
gear he --cp --grm test --pheno test.phe --mpheno 1 --covar test.cov --covar-number 1 3 --keep keep.txt --out he-test
gear he -ss --grm-list mgrm.txt --pheno test.phe --covar test.cov --covar-number 1 2 3 --keep keep.txt --out mgrm
This work has been cited by
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Relationship between LD Score and Haseman-Elston Regression, bioRxiv, 2015
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