Inference of SNP-Gene Regulatory Networks by Integrating Gene Expressions and Genetic Perturbations

Algorithm 2

Optimization for adaptive lasso as a subroutine of Step 3.

(1)  procedure ADAPTIVE LASSO(𝑌,𝑋,𝜆₁,𝜆₂,𝑖,𝛼,𝛽,𝐛_𝑖,𝐟_𝑖̂)⊳𝜆₁ and 𝜆₂ are optimal parameters preliminary

  estimated by cross validation

(2)  Compute 𝐰^𝑏_𝑖 and 𝐰^𝑓_𝑖 (𝑤^𝑏_𝑖𝑗=(𝑏̂_𝑖𝑗)^−𝛼,𝑤^𝑓_𝑖𝑗=(𝑓_𝑖𝑗)^−𝛽)

(3)  while  err>𝜀  do

(4)   𝐛^old_𝑖=𝐛_𝑖,𝐟^old_𝑖=𝐟_𝑖

(5)   for  𝑗←1,𝑀_𝑔  do

(6)    Update 𝑏_𝑖𝑗 via (19)

(7)   end for

(8)   for  𝑗←1,𝑀_𝑠  do

(9)    Update 𝑓_𝑖𝑗 via (20)

(10)  end for

(11)   err=𝐛^old_𝑖−𝐛_𝑖2+𝐟^old_𝑖−𝐟_𝑖2

(12)  end while

(13)  return  𝐛_𝑖 and 𝐟_𝑖

(14) end procedure