Merge branch 'master' into devel

* master: update news Fix issue #170 Add spectrapply method and backend option Fix unit test error due to recent changes Add bpi method (issue #168) set filename only when input is a character Update readMSnSet2 to save filename Cite Lazar 2016 in vignette imputation section add imputatation paper to bib update news and description fix typo in impute man page new github devel version From: Laurent <lg390@cam.ac.uk> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@124452 bc3139a8-67e5-0310-9ffc-ced21a209358
lgatto · Nov 24, 2016 · bafc37a · bafc37a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MSnbase
 Title: Base Functions and Classes for MS-based Proteomics
-Version: 2.1.0
+Version: 2.1.2
 Description: Basic plotting, data manipulation and processing
 	     of MS-based Proteomics data.
 Authors@R: c(person(given = "Laurent", family = "Gatto",

diff --git a/NEWS b/NEWS
@@ -1,3 +1,22 @@
+CHANGES IN VERSION 2.1.2
+------------------------
+ o Update readMSnSet2 to save filename <2016-11-09 Wed>
+ o Ensure that header information is read too if spectra data is
+   loaded for OnDiskMSnExp objects (see issue #170) <2016-11-24 Thu>
+
+CHANGES IN VERSION 2.1.1
+------------------------
+ o Fix typo in impute man page <2016-10-19 Wed>
+ o Cite Lazar 2016 in vignette imputation section <2016-10-28 Fri>
+
+CHANGES IN VERSION 2.1.0
+------------------------
+ o New version for Bioconductor devel
+
+CHANGES IN VERSION 2.0.0
+------------------------
+ o New version for Bioconductor release version 3.4
+
 CHANGES IN VERSION 1.99.6
 -------------------------
  o Reverting to old initialize,Spectrum (see issue #163)

diff --git a/R/readMSnSet.R b/R/readMSnSet.R
@@ -98,6 +98,8 @@ readMSnSet2 <- function(file, ecol, fnames, ...) {
                  paste(colnames(xx), paste = ", "))
         featureNames(ans) <- fdata[, fnames]
     }
+    if (is.character(file)) ## not a data.frame
+        ans@processingData@files <- file
     if (validObject(ans))
         return(ans)
 }
diff --git a/man/impute-methods.Rd b/man/impute-methods.Rd
@@ -203,10 +203,17 @@ Cosmin Lazar (2015). imputeLCMD: A collection of methods for
 left-censored missing data imputation. R package version
 2.0. \url{http://CRAN.R-project.org/package=imputeLCMD}.
 
+Lazar C, Gatto L, Ferro M, Bruley C, Burger T. Accounting for the
+Multiple Natures of Missing Values in Label-Free Quantitative Proteomics
+Data Sets to Compare Imputation Strategies. J Proteome Res. 2016 Apr
+1;15(4):1116-25. doi: 10.1021/acs.jproteome.5b00981. PubMed PMID:
+26906401.
+
 }
 
 \author{
   Laurent Gatto and Samuel Wieczorek
 }
 
 \keyword{methods}
+
diff --git a/vignettes/MSnbase-demo.Rnw b/vignettes/MSnbase-demo.Rnw
@@ -1064,8 +1064,8 @@ table(is.na(x))
 @
 
 
-There are two types of mechanisms resulting in missing values in
-LC/MSMS experiments.
+As described in more details in \cite{Lazar:2016}, there are two types
+of mechanisms resulting in missing values in LC/MSMS experiments.
 
 \begin{itemize}
 \item Missing values resulting from absence of detection of a feature,