version 2.13.5 (2023-09-20)

- Minor update in no-spikes code to avoid re-calculating a constant quantity.
Does not affect output.

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: BASiCS
 Type: Package
 Title: Bayesian Analysis of Single-Cell Sequencing data
-Version: 2.13.4
-Date: 2023-06-26
+Version: 2.13.5
+Date: 2023-09-20
 Authors@R: c(person("Catalina", "Vallejos", role=c("aut", "cre"),
         email="[email protected]",
         comment=c(ORCID = "0000-0003-3638-1960")), 

NEWS

@@ -1678,4 +1678,8 @@ version 2.13.2 (2023-06-16)
 - Changes `LazyData` to `true` to avoid errors 
 
 version 2.13.3 (2023-06-16)
-- Reverts `LazyData` to `false` based on BiocCheck feedback
+- Reverts `LazyData` to `false` based on BiocCheck feedback
+
+version 2.13.5 (2023-09-20)
+- Minor update in no-spikes code to avoid re-calculating a constant quantity.
+Does not affect output. 

R/BASiCS_MCMC.R

@@ -370,7 +370,7 @@ BASiCS_MCMC <- function(
 
   NoSpikeArgs <- list(
     sumByCellAll = sum.bycell.all,
-    Constrain = ArgsDef$Constrain,
+    SizeTimesConstrain = length(ArgsDef$ConstrainGene) * ArgsDef$Constrain,
     Index = ArgsDef$Index,
     RefGene = ArgsDef$RefGene,
     RefGenes = ArgsDef$RefGenes,

R/RcppExports.R

@@ -9,16 +9,16 @@
     .Call('_BASiCS_BASiCS_MCMCcpp', PACKAGE = 'BASiCS', N, Thin, Burn, Counts, BatchDesign, muSpikes, mu0, delta0, phi0, s0, nu0, theta0, mu_mu, s2mu, adelta, bdelta, s2delta, prior_delta, aphi, as, bs, atheta, btheta, ar, LSmu0, LSdelta0, LSphi0, LSnu0, LStheta0, sumByCellBio, sumByGeneAll, sumByGeneBio, StoreAdapt, EndAdapt, PrintProgress, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, threads)
 }
 
-.BASiCS_MCMCcppNoSpikes <- function(N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, adelta, bdelta, s2delta, prior_delta, as, bs, atheta, btheta, Constrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads = 1L) {
-    .Call('_BASiCS_BASiCS_MCMCcppNoSpikes', PACKAGE = 'BASiCS', N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, adelta, bdelta, s2delta, prior_delta, as, bs, atheta, btheta, Constrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads)
+.BASiCS_MCMCcppNoSpikes <- function(N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, adelta, bdelta, s2delta, prior_delta, as, bs, atheta, btheta, SizeTimesConstrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads = 1L) {
+    .Call('_BASiCS_BASiCS_MCMCcppNoSpikes', PACKAGE = 'BASiCS', N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, adelta, bdelta, s2delta, prior_delta, as, bs, atheta, btheta, SizeTimesConstrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads)
 }
 
 .BASiCS_MCMCcppReg <- function(N, Thin, Burn, Counts, BatchDesign, muSpikes, mu0, delta0, phi0, s0, nu0, theta0, mu_mu, s2mu, aphi, as, bs, atheta, btheta, k, m0, V0, sigma2_a0, sigma2_b0, beta0, sigma20, eta0, lambda0, variance, ar, LSmu0, LSdelta0, LSphi0, LSnu0, LStheta0, sumByCellBio, sumByGeneAll, sumByGeneBio, StoreAdapt, EndAdapt, PrintProgress, FixLocations, RBFMinMax, RBFLocations, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, threads = 1L) {
     .Call('_BASiCS_BASiCS_MCMCcppReg', PACKAGE = 'BASiCS', N, Thin, Burn, Counts, BatchDesign, muSpikes, mu0, delta0, phi0, s0, nu0, theta0, mu_mu, s2mu, aphi, as, bs, atheta, btheta, k, m0, V0, sigma2_a0, sigma2_b0, beta0, sigma20, eta0, lambda0, variance, ar, LSmu0, LSdelta0, LSphi0, LSnu0, LStheta0, sumByCellBio, sumByGeneAll, sumByGeneBio, StoreAdapt, EndAdapt, PrintProgress, FixLocations, RBFMinMax, RBFLocations, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, threads)
 }
 
-.BASiCS_MCMCcppRegNoSpikes <- function(N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, as, bs, atheta, btheta, k, m0, V0, sigma2_a0, sigma2_b0, beta0, sigma20, eta0, lambda0, variance, Constrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, RBFMinMax, FixLocations, RBFLocations, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads = 1L) {
-    .Call('_BASiCS_BASiCS_MCMCcppRegNoSpikes', PACKAGE = 'BASiCS', N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, as, bs, atheta, btheta, k, m0, V0, sigma2_a0, sigma2_b0, beta0, sigma20, eta0, lambda0, variance, Constrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, RBFMinMax, FixLocations, RBFLocations, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads)
+.BASiCS_MCMCcppRegNoSpikes <- function(N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, as, bs, atheta, btheta, k, m0, V0, sigma2_a0, sigma2_b0, beta0, sigma20, eta0, lambda0, variance, SizeTimesConstrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, RBFMinMax, FixLocations, RBFLocations, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads = 1L) {
+    .Call('_BASiCS_BASiCS_MCMCcppRegNoSpikes', PACKAGE = 'BASiCS', N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, as, bs, atheta, btheta, k, m0, V0, sigma2_a0, sigma2_b0, beta0, sigma20, eta0, lambda0, variance, SizeTimesConstrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, RBFMinMax, FixLocations, RBFLocations, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads)
 }
 
 .muUpdate <- function(mu0, prop_var, Counts, invdelta, phinu, sum_bycell_bio, mu_mu, s2_mu, q0, n, mu1, u, ind, exponent, mintol) {
@@ -45,8 +45,8 @@
     .Call('_BASiCS_thetaUpdateBatch', PACKAGE = 'BASiCS', theta0, prop_var, BatchDesign, BatchSizes, s, nu, a_theta, b_theta, n, nBatch, exponent, mintol)
 }
 
-.muUpdateNoSpikes <- function(mu0, prop_var, Counts, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, Constrain, RefGene, ConstrainGene, NotConstrainGene, exponent, mintol) {
-    .Call('_BASiCS_muUpdateNoSpikes', PACKAGE = 'BASiCS', mu0, prop_var, Counts, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, Constrain, RefGene, ConstrainGene, NotConstrainGene, exponent, mintol)
+.muUpdateNoSpikes <- function(mu0, prop_var, Counts, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, SizeTimesConstrain, RefGene, ConstrainGene, NotConstrainGene, exponent, mintol) {
+    .Call('_BASiCS_muUpdateNoSpikes', PACKAGE = 'BASiCS', mu0, prop_var, Counts, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, SizeTimesConstrain, RefGene, ConstrainGene, NotConstrainGene, exponent, mintol)
 }
 
 .nuUpdateBatchNoSpikes <- function(nu0, prop_var, Counts, BatchDesign, mu, invdelta, s, thetaBatch, sum_bygene_all, q0, n, nu1, u, ind, exponent, mintol) {
@@ -81,8 +81,8 @@
     .Call('_BASiCS_lambdaUpdateReg', PACKAGE = 'BASiCS', delta, X, beta, sigma2, eta, q0, lambda1, exponent)
 }
 
-.muUpdateRegNoSpikes <- function(mu0, prop_var, Counts, delta, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, Constrain, RefGene, ConstrainGene, NotConstrainGene, k, lambda, beta, X, sigma2, variance, FixLocations, RBFMinMax, RBFLocations, exponent, mintol) {
-    .Call('_BASiCS_muUpdateRegNoSpikes', PACKAGE = 'BASiCS', mu0, prop_var, Counts, delta, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, Constrain, RefGene, ConstrainGene, NotConstrainGene, k, lambda, beta, X, sigma2, variance, FixLocations, RBFMinMax, RBFLocations, exponent, mintol)
+.muUpdateRegNoSpikes <- function(mu0, prop_var, Counts, delta, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, SizeTimesConstrain, RefGene, ConstrainGene, NotConstrainGene, k, lambda, beta, X, sigma2, variance, FixLocations, RBFMinMax, RBFLocations, exponent, mintol) {
+    .Call('_BASiCS_muUpdateRegNoSpikes', PACKAGE = 'BASiCS', mu0, prop_var, Counts, delta, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, SizeTimesConstrain, RefGene, ConstrainGene, NotConstrainGene, k, lambda, beta, X, sigma2, variance, FixLocations, RBFMinMax, RBFLocations, exponent, mintol)
 }
 
 .deltaUpdateRegNoSpikes <- function(delta0, prop_var, Counts, mu, nu, q0, n, delta1, u, ind, lambda, X, sigma2, beta, exponent, mintol) {

src/MCMCNoSpikes.h

@@ -71,7 +71,7 @@ Rcpp::List BASiCS_MCMCcppNoSpikes(
     double bs,
     double atheta, 
     double btheta, 
-    double Constrain,
+    double SizeTimesConstrain,
     arma::vec Index,
     int RefGene,
     arma::vec RefGenes,
@@ -244,8 +244,11 @@ Rcpp::List BASiCS_MCMCcppNoSpikes(
         arma::randi(1, arma::distr_param(0, RefGenes.size() - 1))
       );
       RefGene = RefGenes(RefAux); 
+      Rcpp::Rcout << "RefGene: " << RefGene << std::endl;
+
       if (i >= Burn) RefFreq(RefGene) += 1;
     }
+
     muAux = muUpdateNoSpikes(
       muAux.col(0),
       exp(LSmuAux),
@@ -260,7 +263,7 @@ Rcpp::List BASiCS_MCMCcppNoSpikes(
       y_q0,
       u_q0,
       ind_q0,
-      Constrain,
+      SizeTimesConstrain,
       RefGene,
       ConstrainGene_uvec, 
       NotConstrainGene_uvec,
@@ -270,6 +273,7 @@ Rcpp::List BASiCS_MCMCcppNoSpikes(
     PmuAux += muAux.col(1);
     if(i>=Burn) {muAccept += muAux.col(1);}  
 
+
     // UPDATE OF DELTA: 
     // 1st COLUMN IS THE UPDATE, 
     // 2nd COLUMN IS THE ACCEPTANCE INDICATOR
@@ -363,6 +367,7 @@ Rcpp::List BASiCS_MCMCcppNoSpikes(
       }
     }
 
+
     // PRINT IN CONSOLE SAMPLED VALUES FOR FEW SELECTED PARAMETERS
     if((i%(2*Thin) == 0) & (PrintProgress == 1)) {
       CurrentIter(i, N);      

src/MCMCRegNoSpikes.h

@@ -74,7 +74,7 @@ Rcpp::List BASiCS_MCMCcppRegNoSpikes(
     double eta0, 
     arma::vec lambda0, 
     double const& variance,
-    double Constrain,
+    double SizeTimesConstrain,
     arma::vec Index,
     int RefGene,
     arma::vec RefGenes,
@@ -286,6 +286,9 @@ Rcpp::List BASiCS_MCMCcppRegNoSpikes(
         RefFreq(RefGene) += 1;
       }
     }
+    Rcpp::Rcout << "Iteration: " << i << std::endl;
+    Rcpp::Rcout << "RefGene: " << RefGene+1 << std::endl;
+    Rcpp::Rcout << "RefGene before update: " << muAux(0, 0) << std::endl;
     muAux = muUpdateRegNoSpikes(
       muAux.col(0),
       exp(LSmuAux),
@@ -300,7 +303,7 @@ Rcpp::List BASiCS_MCMCcppRegNoSpikes(
       y_q0,
       u_q0,
       ind_q0,
-      Constrain,
+      SizeTimesConstrain,
       RefGene,
       ConstrainGene_uvec,
       NotConstrainGene_uvec,
@@ -317,6 +320,7 @@ Rcpp::List BASiCS_MCMCcppRegNoSpikes(
       mintol_mu
     );
     PmuAux += muAux.col(1); if(i>=Burn) muAccept += muAux.col(1);
+    Rcout << "RefGene after update: " << muAux(RefGene, 0) << std::endl;
 
     // UPDATE OF DELTA: 
     // 1st COLUMN IS THE UPDATE,