all examples now use the BdistachyonTechnical data set from metaboData

aberHRML · Sep 27, 2021 · 1551a16 · 1551a16
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -69,7 +69,6 @@ jobs:
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran(c("rcmdcheck","goodpractice"))
-          metaboData::downloadDataSet('FIE-HRMS','BdistachyonEcotypes',ask = FALSE)
         shell: Rscript {0}
 
       - name: Check

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,7 @@ Imports:
     furrr
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Collate:
     allGenerics.R
     allClasses.R

diff --git a/R/binneRlyse.R b/R/binneRlyse.R
@@ -18,10 +18,9 @@
 #' @seealso \code{\link{Binalysis-class}}, \code{\link{binParameters}}, 
 #' \code{\link{sampleInfo}}, \code{\link{binnedData}},  \code{\link{accurateData}}
 #' @examples 
-#' \dontrun{
-#' files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')
+#' files <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')
 #' 
-#' info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')
+#' info <- metaboData::runinfo('FIE-HRMS','BdistachyonTechnical')
 #' 
 #' parameters <- detectParameters(files)
 #' cls(parameters) <- 'class'
@@ -32,7 +31,6 @@
 #' analysis <- binneRlyse(files, 
 #'                        info, 
 #'                        parameters = parameters)
-#'    }
 #' @importFrom dplyr ungroup n
 #' @importFrom magrittr %>%
 #' @importFrom crayon blue red green

diff --git a/R/detect.R b/R/detect.R
@@ -9,7 +9,7 @@
 #' if (requireNamespace("metaboData", quietly = TRUE)) {
 #'    detectInfusionScans(
 #'       metaboData::filePaths('FIE-HRMS',
-#'                             'BdistachyonEcotypes',
+#'                             'BdistachyonTechnical',
 #'                             ask = FALSE)[1])
 #' }
 #' @importFrom mzR openMSfile header
@@ -71,7 +71,7 @@ detectInfusionScans <- function(files,
 #' @param files character vector of file paths
 #' @return S4 object of class BinParameters
 #' @examples 
-#' files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')
+#' files <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')
 #' parameters <- detectParameters(files[1])
 #' @seealso \code{\link{BinParameters-class}}, \code{\link{binParameters}}
 #' @export

diff --git a/R/plot.R b/R/plot.R
@@ -138,7 +138,7 @@ setMethod('plotChromatogram',signature = 'Binalysis',
 #' @param files character vector of file paths to use
 #' @param scans specify scans to highlight within the plot
 #' @examples 
-#' plotChromFromFile(metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1],
+#' plotChromFromFile(metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')[1],
 #'                             scans = c(6,18))
 #' @export
 

diff --git a/R/readFiles.R b/R/readFiles.R
@@ -14,7 +14,7 @@
 #' @examples 
 #' ## Example file path
 #' file_paths <- metaboData::filePaths('FIE-HRMS',
-#'                                     'BdistachyonEcotypes')[1]
+#'                                     'BdistachyonTechnical')[1]
 #' 
 #' ## Optionally declare parallel processing backend
 #' # plan(future::multisession,workers = 2)

diff --git a/R/singleSample.R b/R/singleSample.R
@@ -15,7 +15,7 @@
 #' \code{binner_dp} or the environment variable \code{BINNER_DP}.
 #' 
 #' @examples 
-#' file_path <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1]
+#' file_path <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')[1]
 #' 
 #' ## Optionally declare parallel processing backend
 #' # plan(future::multisession,workers = 2)

diff --git a/man/binneRlyse.Rd b/man/binneRlyse.Rd
diff --git a/man/detectInfusionScans.Rd b/man/detectInfusionScans.Rd
diff --git a/man/detectParameters.Rd b/man/detectParameters.Rd
diff --git a/man/plotChromFromFile.Rd b/man/plotChromFromFile.Rd
diff --git a/man/readFiles.Rd b/man/readFiles.Rd
diff --git a/man/singleSample.Rd b/man/singleSample.Rd
diff --git a/tests/testthat/test-binneRlyse.R b/tests/testthat/test-binneRlyse.R
@@ -2,7 +2,7 @@
 context('binneRlyse')
 
 file <- metaboData::filePaths('FIE-HRMS',
-																														'BdistachyonEcotypes',
+																														'BdistachyonTechnical',
 																														ask = FALSE)[1]
 
 info <- tibble::tibble(fileOrder = 1,

diff --git a/tests/testthat/test-detectInfusionScans.R b/tests/testthat/test-detectInfusionScans.R
@@ -3,7 +3,7 @@ context('detectInfusionScans')
 
 test_that('detectInfusionScans works',{
 	file <- metaboData::filePaths('FIE-HRMS',
-																															'BdistachyonEcotypes',
+																															'BdistachyonTechnical',
 																															ask = FALSE)[1]
 
 	scans <- detectInfusionScans(file)

diff --git a/tests/testthat/test-detectParameters.R b/tests/testthat/test-detectParameters.R
@@ -4,7 +4,7 @@ context('detectParameters')
 
 test_that('detectParameters works',{
 	files <- metaboData::filePaths('FIE-HRMS',
-																																'BdistachyonEcotypes',
+																																'BdistachyonTechnical',
 																																ask = FALSE)
 
 	parameters <- detectParameters(files[1])

diff --git a/tests/testthat/test-getPeaks.R b/tests/testthat/test-getPeaks.R
@@ -2,7 +2,7 @@
 context('getPeaks')
 
 file <- metaboData::filePaths('FIE-HRMS',
-																														'BdistachyonEcotypes',
+																														'BdistachyonTechnical',
 																														ask = FALSE)[1]
 
 test_that('sampProcess works',{

diff --git a/tests/testthat/test-plotting.R b/tests/testthat/test-plotting.R
@@ -1,7 +1,7 @@
 
 context('measures plots')
 
-file <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1]
+file <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')[1]
 
 info <- tibble::tibble(fileOrder = 1,
 											 injOrder = 1,

diff --git a/tests/testthat/test-readFiles.R b/tests/testthat/test-readFiles.R
@@ -3,7 +3,7 @@ context('readFiles')
 
 test_that('readFiles works',{
 	file <- metaboData::filePaths('FIE-HRMS',
-																															'BdistachyonEcotypes',
+																															'BdistachyonTechnical',
 																															ask = FALSE)[1]
 
 	res <- readFiles(file,dp = 2,scans = 5:13)

diff --git a/tests/testthat/test-singleSample.R b/tests/testthat/test-singleSample.R
@@ -3,7 +3,7 @@ context('singleSample')
 
 test_that('single sample works',{
 	file <- metaboData::filePaths('FIE-HRMS',
-																															'BdistachyonEcotypes',
+																															'BdistachyonTechnical',
 																															ask = FALSE)[1]
 	bd <- singleSample(file,class = 'test',verbose = TRUE)
 
@@ -12,7 +12,7 @@ test_that('single sample works',{
 
 test_that('single sample works with no class specified',{
 	file <- metaboData::filePaths('FIE-HRMS',
-																															'BdistachyonEcotypes',
+																															'BdistachyonTechnical',
 																															ask = FALSE)[1]
 	bd <- singleSample(file,verbose = TRUE)
 
@@ -21,23 +21,23 @@ test_that('single sample works with no class specified',{
 
 test_that('single samples errors with > 1 file',{
 	file <- metaboData::filePaths('FIE-HRMS',
-																															'BdistachyonEcotypes',
+																															'BdistachyonTechnical',
 																															ask = FALSE)[1:2]
 
 	expect_error(singleSample(file,verbose = FALSE))
 })
 
 test_that('single samples errors with > 1 file',{
 	file <- metaboData::filePaths('FIE-HRMS',
-																															'BdistachyonEcotypes',
+																															'BdistachyonTechnical',
 																															ask = FALSE)[1:2]
 
 	expect_error(singleSample(file,verbose = FALSE))
 })
 
 test_that('single samples errors with > 1 class',{
 	file <- metaboData::filePaths('FIE-HRMS',
-																															'BdistachyonEcotypes',
+																															'BdistachyonTechnical',
 																															ask = FALSE)[1]
 
 	expect_error(singleSample(file,class = c('wrong','incorrect'),verbose = FALSE))

diff --git a/vignettes/binneR.Rmd b/vignettes/binneR.Rmd
@@ -36,11 +36,11 @@ library(magrittr)
 ```{r check_example_data,include=FALSE}
 example_data_status <- metaboData::availableDataSets() %>% 
 	filter(technique == 'FIE-HRMS',
-								`data set` == 'BdistachyonEcotypes') %>% 
+								`data set` == 'BdistachyonTechnical') %>% 
 	.$status
 
 if (example_data_status != 'available'){
-	metaboData::downloadDataSet('FIE-HRMS','BdistachyonEcotypes',ask = FALSE)
+	metaboData::downloadDataSet('FIE-HRMS','BdistachyonTechnical',ask = FALSE)
 }
 ```
 
@@ -58,7 +58,7 @@ FIE-HRMS data consists of a 'plug flow', across which MS signal intensities can
 
 ```{r FIEfingerprint, echo=FALSE, fig.width=7,fig.height=5,fig.align='center',fig.show='animate',animation.hook = 'gifski',interval=0.1,dev='png',aniopts=('controls,loop'),message=FALSE}
 
-file <- filePaths('FIE-HRMS','BdistachyonEcotypes')[1]
+file <- filePaths('FIE-HRMS','BdistachyonTechnical')[1]
 ms <- openMSfile(file)
 chrom <- mzR::header(ms)
 
@@ -156,7 +156,7 @@ For a set of specified file paths, the range of infusion scans can be detected u
 
 ```{r infusionScanDetection}
 infusionScans <- detectInfusionScans(
-	metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1],
+	metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')[1],
 	thresh = 0.5
 )
 infusionScans
@@ -167,7 +167,7 @@ The infusion scans can also be plotted by supplying the range to the scans argum
 
 ```{r exampleChromatograms, fig.width=7,fig.height=5,fig.align='center'}
 plotChromFromFile(
-	metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1],
+	metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')[1],
 	scans = infusionScans
 )
 ```
@@ -180,7 +180,7 @@ Spectral binning can be performed using the `readFiles()` function as shown belo
 The example file within the package can be specified using the following.
 
 ```{r fileList}
-file <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1]
+file <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')[1]
 ```
 
 Then the data can be spectrally binned using:
@@ -203,16 +203,16 @@ Some bin measures are also computed that allow the assessment of the quality of
 Subsequent analyses of these data can easily be applied using the [*metabolyseR*](https://github.com/jasenfinch/metabolyseR) package.
 The [*metaboWorkflows*](https://github.com/jasenfinch/metaboWorkflows) package also provides customisable wrapper workflows for high resolution FIE-MS analyses.
 
-The example data used here is from the [*metaboData*](https://github.com/aberHRML/metaboData) package and consists of a comparison of leaf tissue from four *B. distachyon* ecotypes.
+The example data used here is from the [*metaboData*](https://github.com/aberHRML/metaboData) package and consists 10 replicate injections of a leaf tissue extract from the model grass species *Brachypodium distachyon*.
 
 ### Basic Usage
 
 Firstly the file paths and sample information can be loaded for the example data set using the following:
 
 ```{r exampleFiles}
-info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')
+info <- metaboData::runinfo('FIE-HRMS','BdistachyonTechnical')
 
-files <-  metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')
+files <-  metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')
 ```
 
 There are two main functions for processing experimental data: