Merge pull request #51 from aberHRML/devel

v2.5.2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: binneR
 Title: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
-Version: 2.5.1
+Version: 2.5.2
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: A spectral binning approach for high resolution flow infusion mass spectrometry data.
 biocViews: MassSpectrometry, Metabolomics

NAMESPACE

@@ -80,6 +80,7 @@ importFrom(magrittr,"%>%")
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_names)
 importFrom(methods,show)
+importFrom(mzR,close)
 importFrom(mzR,header)
 importFrom(mzR,openMSfile)
 importFrom(mzR,peaks)

NEWS.md

@@ -1,3 +1,9 @@
+# binneR v2.5.2
+
+* Fixed I/O issues for sample sets over ~1200.
+
+* Minor alteration to console output
+
 # binneR v2.5.1
 
 * Performance and memory usage gains through ensuring 0 values are not read from raw files.

R/detect.R

@@ -20,9 +20,13 @@ detectInfusionScans <- function(files,
 
 	ms <- files %>%
 		future_map(~{
-			.x %>%
-				openMSfile() %>%
+			ms <- .x %>%
+				openMSfile()
+
+			file_header <- ms %>%
 				header()
+
+			return(file_header)
 		}) %>%
 		set_names(files)
 

R/get.R

@@ -1,4 +1,3 @@
-#' @importFrom mzR openMSfile peaks
 #' @importFrom stats aggregate
 #' @importFrom dplyr bind_rows group_by summarise
 #' @importFrom magrittr %>%
@@ -13,7 +12,7 @@ sampProcess <- function(file,scans,dp){
     return(pl)
 }
 
-#' @importFrom mzR openMSfile peaks
+#' @importFrom mzR openMSfile peaks close
 #' @importFrom purrr map
 #' @importFrom dplyr bind_rows
 #' @importFrom tibble as_tibble
@@ -32,7 +31,7 @@ getFile <- function(file,scans){
     hd$polarity[hd$polarity == 0] <- 'n'
     hd$polarity[hd$polarity == 1] <- 'p'
 
-    ms %>%
+    file_peaks <- ms %>%
         peaks() %>%
         .[hd$seqNum] %>%
         map(~{
@@ -47,6 +46,8 @@ getFile <- function(file,scans){
         mutate(seqNum = as.numeric(seqNum)) %>%
         left_join(hd, by = "seqNum") %>%
         select(-filterString,-seqNum)
+
+    return(file_peaks)
 }
 
 #' @importFrom parallel makeCluster stopCluster parLapply clusterExport
@@ -68,9 +69,13 @@ getHeaders <- function(files){
 
     headers <- files %>% 
         future_map(~{
-        .x %>%
-            openMSfile(backend = 'pwiz') %>%
+        ms <- .x %>%
+            openMSfile(backend = 'pwiz') 
+
+        file_header <- ms %>%
             header()
+
+        return(file_header)
     }) %>%
         set_names(files) %>%
         bind_rows(.id = 'FileName') %>%

R/spectralBinning-method.R

@@ -16,7 +16,7 @@ setMethod("spectralBinning",
 						if (isTRUE(verbose)) message('Reading raw data')
 						pks <- getPeaks(files,scans(x))
 
-						if (isTRUE(verbose)) message('Calculating bins')
+						if (isTRUE(verbose)) message('Gathering bins')
 						bin_list <- calcBinList(pks)
 
 						if (isTRUE(verbose)) message('Removing single scan events')
@@ -65,7 +65,7 @@ setMethod("spectralBinning",
 							}) %>%
 							bind_rows()
 
-						if (isTRUE(verbose)) message('Calculating bin measures')
+						if (isTRUE(verbose)) message('Calculating bin metrics')
 						bin_measures <- calcBinMeasures(pks,
 																					 cls)
 
@@ -96,6 +96,7 @@ setMethod("spectralBinning",
 									select(-fileName,-polarity)
 							})
 
+						if (isTRUE(verbose)) message('Gathering file headers')
 						headers <- getHeaders(files)
 
 						binnedData(x) <- binned_data

docs/articles/binneR_files/header-attrs-2.7/header-attrs.js

@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});

docs/pkgdown.yml

@@ -1,7 +1,7 @@
-pandoc: 2.7.3
+pandoc: 2.11.2
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   binneR: binneR.html
-last_built: 2020-11-20T02:16Z
+last_built: 2021-03-06T01:01Z