From f2c84f30a1e631936d7df20c259c30b7785640b9 Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Fri, 9 Sep 2016 12:43:38 +0200
Subject: [PATCH] after rmReact columns in rxnGeneMatrix and allGenes didnt
match
---
R/rmReact.R | 16 ++--------------
inst/NEWS.Rd | 2 ++
2 files changed, 4 insertions(+), 14 deletions(-)
diff --git a/R/rmReact.R b/R/rmReact.R
index 0efb32c..c420d70 100644
--- a/R/rmReact.R
+++ b/R/rmReact.R
@@ -162,21 +162,9 @@ rmReact <- function(model, react, rm_met = TRUE) {
ag <- ag[which(ncag != 0)]
allGenes(mod_out) <- ag
}
- #TODO: update indices in the GPR rules accoording to the updated allGenes slot!
-
- # reaction to gene mapping
- #SrGMbin <- rxnGeneMat(mod_out) != 0
-
- #SrGMbindiag <- diag(crossprod(SrGMbin))
-
- #keepGenes <- ifelse(SrGMbindiag == 0, FALSE, TRUE)
- keepGenes <- sapply(allGenes(model), function(x) match(x, allGenes(mod_out)))
- keepGenes <- ifelse(is.na(keepGenes), FALSE, TRUE)
- #print(keepGenes)
-
- rxnGeneMat(mod_out) <- rxnGeneMat(mod_out)[, keepGenes, drop = FALSE]
- #print(dim(rxnGeneMat))
+ newGeneOrder <- match(allGenes(mod_out), allGenes(model))
+ rxnGeneMat(mod_out) <- rxnGeneMat(mod_out)[, newGeneOrder, drop = FALSE]
}
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 9f9fd1f..7e44a59 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -8,6 +8,8 @@
\section{Changes in version 2.0.1 2016-07-05}{
\itemize{
+ \item After \code{rmReact} the columns of \code{rxnGeneMat} and
+ \code{allGenes}-slot did not match.
\item \code{upgradeModelorg} was not working correctly, when all gprRules
are empty.
}
--
GitLab