diff --git a/Deconvolution/BLADE.py b/Deconvolution/BLADE.py index 90942af..afe7b56 100755 --- a/Deconvolution/BLADE.py +++ b/Deconvolution/BLADE.py @@ -180,7 +180,7 @@ def grad_Nu(Y, SigmaY, Nu, Omega, Beta, Mu0, Alpha0, Beta0, Kappa0, Ngene, Ncell NuExp = np.sum(Nu, 0)/Nsample Diff = np.zeros((Ngene, Ncell)) - ExpBetaN = Beta0 + Nsample*(Nsample+3)/2*np.square(Omega) + \ + ExpBetaN = Beta0 + (Nsample-1)/2*np.square(Omega) + \ Kappa0*Nsample/(2*(Kappa0 + Nsample)) * (np.square(Omega)/Nsample + np.square(NuExp - Mu0)) for i in range(Nsample): @@ -278,13 +278,13 @@ def grad_Omega(Y, SigmaY, Nu, Omega, Beta, Mu0, Alpha0, Beta0, Kappa0, Ngene, Nc # gradient of PX (first term) AlphaN = Alpha0 + Nsample * 0.5 NuExp = np.sum(Nu, 0)/Nsample - ExpBetaN = Beta0 + Nsample*(Nsample+3)/2*np.square(Omega) + \ + ExpBetaN = Beta0 + (Nsample-1)/2*np.square(Omega) + \ Kappa0*Nsample/(2*(Kappa0 + Nsample)) * (np.square(Omega)/Nsample + np.square(NuExp - Mu0)) for i in range(Nsample): ExpBetaN = ExpBetaN + 0.5*np.square(Nu[i,:,:] - NuExp) - Nominator = - AlphaN * Nsample*(Nsample+3)*Omega + Kappa0 /(Kappa0 + Nsample) * Omega + Nominator = - AlphaN * (Nsample-1)*Omega + Kappa0 /(Kappa0 + Nsample) * Omega grad_PX = Nominator / ExpBetaN @@ -565,7 +565,7 @@ def Estep_PX(Mu0, Nu, Omega, Alpha0, Beta0, Kappa0, Ncell, Nsample): NuExp = np.sum(Nu, 0)/Nsample # expected Nu, Ngene by Ncell AlphaN = Alpha0 + 0.5*Nsample # Posterior Alpha - ExpBetaN = Beta0 + Nsample*(Nsample+3)/2*np.square(Omega) + \ + ExpBetaN = Beta0 + (Nsample-1)/2*np.square(Omega) + \ Kappa0*Nsample/(2*(Kappa0 + Nsample)) * (np.square(Omega)/Nsample + np.square(NuExp - Mu0)) for i in range(Nsample): diff --git a/LICENSE b/LICENSE old mode 100644 new mode 100755 diff --git a/PGFdeconvolution/LogNormalvsNB_TCGA.R b/PGFdeconvolution/LogNormalvsNB_TCGA.R old mode 100644 new mode 100755 diff --git a/PGFdeconvolution/LogNormalvsNB_TCGA.html b/PGFdeconvolution/LogNormalvsNB_TCGA.html old mode 100644 new mode 100755 diff --git a/PGFdeconvolution/README.md b/PGFdeconvolution/README.md old mode 100644 new mode 100755 diff --git a/PGFdeconvolution/TCGA-MESO.RData b/PGFdeconvolution/TCGA-MESO.RData old mode 100644 new mode 100755 diff --git a/PGFdeconvolution/TCGA-SARC.RData b/PGFdeconvolution/TCGA-SARC.RData old mode 100644 new mode 100755 diff --git a/PGFdeconvolution/install.R b/PGFdeconvolution/install.R old mode 100644 new mode 100755 diff --git a/PGFdeconvolution/source_estmusigmadist2.R b/PGFdeconvolution/source_estmusigmadist2.R old mode 100644 new mode 100755 diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/Singularity b/Singularity old mode 100644 new mode 100755 diff --git a/data/.keep b/data/.keep old mode 100644 new mode 100755 diff --git a/environment.yml b/environment.yml old mode 100644 new mode 100755 diff --git a/framework.png b/framework.png old mode 100644 new mode 100755 diff --git a/jupyter/BLADE - Demo script.ipynb b/jupyter/BLADE - Demo script.ipynb old mode 100644 new mode 100755 diff --git a/logo_final_small.png b/logo_final_small.png old mode 100644 new mode 100755 diff --git a/setup.py b/setup.py old mode 100644 new mode 100755 index b2fbf46..8fbe393 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="BLADE-Deconvolution", - version="0.0.5", + version="0.0.6", author="Yongsoo Kim", author_email="anoyaro84@gmail.com", description="BLADE (Bayesian Log-normAl DEconvolution)",