HELink

Haseman-Elston regression for linkage analysis with heterogeneity in parental effects

---

Master option
--he-link

option
--bfile <args>
Specify the binary format family data.

--he-joint
If this option is on, paternal and maternal ibd will be estimated jointly.

--ibd
Specify the ibd file. A quick IBD inference algorithm has been proposed in GEAR. Link to quick ibd algorithm.

--pheno
Specify the phenotype file

--sd, --cp, --ss
Specify the means the phenotype is coded for the joint HE regression.
--sd indicates squared difference; y_ij = (y_i - y_j) * (y_i - y_j).
--cp indicates cross products; y_ij = y_i * y_j.
--ss indicates sum of squares. y_ij = (y_i + y_j) * (y_i + y_j)
By default, --sd will be used.

Examples

gear --he-link --bfile test --ibd test.ibd --phe test.phe --out
gear --he-link --he-joint --bfile test --ibd test.ibd --phe test.phe --out

gear --he-link --cp --bfile test --ibd test.ibd --phe test.phe --out
gear --he-link --ss --he-joint --bfile test --ibd test.ibd --phe test.phe --out

Download example files