[med-svn] [r-bioc-deseq2] 01/06: New upstream version 1.14.1

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-deseq2.

commit a9c33f5cda06b75407238f9abb0f82508e72b8ac
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 4 14:10:09 2016 +0100

    New upstream version 1.14.1
---
 DESCRIPTION         |   4 ++--
 NEWS                |   5 +++++
 build/vignette.rds  | Bin 231 -> 231 bytes
 inst/doc/DESeq2.pdf | Bin 673682 -> 672224 bytes
 src/DESeq2.cpp      |  10 +++++-----
 5 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index af2bd06..fb3ae36 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: DESeq2
 Type: Package
 Title: Differential gene expression analysis based on the negative
         binomial distribution
-Version: 1.14.0
+Version: 1.14.1
 Author: Michael Love, Simon Anders, Wolfgang Huber
 Maintainer: Michael Love <michaelisaiahlove at gmail.com>
 Description: Estimate variance-mean dependence in count data from
@@ -22,4 +22,4 @@ biocViews: Sequencing, ChIPSeq, RNASeq, SAGE, DifferentialExpression,
         GeneExpression, Transcription
 RoxygenNote: 5.0.1
 NeedsCompilation: yes
-Packaged: 2016-10-17 23:12:25 UTC; biocbuild
+Packaged: 2016-12-01 00:14:26 UTC; biocbuild
diff --git a/NEWS b/NEWS
index 512a034..09b5455 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,8 @@
+CHANGES IN VERSION 1.14.1
+-------------------------
+
+    o Removed deprecated armadillo argument in DESeq2.cpp
+
 CHANGES IN VERSION 1.13.8
 -------------------------
 
diff --git a/build/vignette.rds b/build/vignette.rds
index a30845c..13dfd64 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/DESeq2.pdf b/inst/doc/DESeq2.pdf
index 0c61266..40d0612 100644
Binary files a/inst/doc/DESeq2.pdf and b/inst/doc/DESeq2.pdf differ
diff --git a/src/DESeq2.cpp b/src/DESeq2.cpp
index 0efa29a..8fc4508 100644
--- a/src/DESeq2.cpp
+++ b/src/DESeq2.cpp
@@ -56,7 +56,7 @@ double dlog_posterior(double log_alpha, Rcpp::NumericMatrix::Row y, Rcpp::Numeri
   arma::mat dw = arma::diagmat(Rcpp::as<arma::vec>(dw_diag));
   arma::mat b = x.t() * w * x;
   arma::mat db = x.t() * dw * x;
-  double ddetb = ( det(b) * trace(b.i(true) * db) );
+  double ddetb = ( det(b) * trace(b.i() * db) );
   double cr_term = -0.5 * ddetb / det(b);
   double alpha_neg1 = R_pow_di(alpha, -1);
   double alpha_neg2 = R_pow_di(alpha, -2);
@@ -84,10 +84,10 @@ double d2log_posterior(double log_alpha, Rcpp::NumericMatrix::Row y, Rcpp::Numer
   Rcpp::NumericVector d2w_diag = 2 * pow(pow(mu, -1) + alpha, -3);
   arma::mat d2w = arma::diagmat(as<arma::vec>(d2w_diag));
   arma::mat b = x.t() * w * x;
-  arma::mat b_i = b.i(true);
+  arma::mat b_i = b.i();
   arma::mat db = x.t() * dw * x;
   arma::mat d2b = x.t() * d2w * x;
-  double ddetb = ( det(b) * trace(b.i(true) * db) );
+  double ddetb = ( det(b) * trace(b.i() * db) );
   double d2detb = ( det(b) * (R_pow_di(trace(b_i * db), 2) - trace(b_i * db * b_i * db) + trace(b_i * d2b)) );
   double cr_term = 0.5 * R_pow_di(ddetb/det(b), 2) - 0.5 * d2detb / det(b); 
   double alpha_neg1 = R_pow_di(alpha, -1);
@@ -345,10 +345,10 @@ Rcpp::List fitBeta(SEXP ySEXP, SEXP xSEXP, SEXP nfSEXP, SEXP alpha_hatSEXP, SEXP
     beta_mat.row(i) = beta_hat.t();
     // recalculate w so that this is identical if we start with beta_hat
     w = diagmat(mu_hat/(1.0 + alpha_hat[i] * mu_hat));
-    hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
+    hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i() * x.t() * sqrt(w);
     hat_diagonals.row(i) = diagvec(hat_matrix).t();
     // sigma is the covariance matrix for the betas
-    sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
+    sigma = (x.t() * w * x + ridge).i() * x.t() * w * x * (x.t() * w * x + ridge).i();
     contrast_num.row(i) = contrast.t() * beta_hat;
     contrast_denom.row(i) = sqrt(contrast.t() * sigma * contrast);
     beta_var_mat.row(i) = diagvec(sigma).t();

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