Title: | Example Metabolomics Data Sets |
---|---|
Description: | Data sets from a variety of biological sample matrices, analysed using a number of mass spectrometry based metabolomic analytical techniques. The example data sets are stored remotely using GitHub releases <https://github.com/aberHRML/metaboData/releases> which can be accessed from R using the package. The package also includes the 'abr1' FIE-MS data set from the 'FIEmspro' package <https://users.aber.ac.uk/jhd/> <doi:10.1038/nprot.2007.511>. |
Authors: | Jasen Finch [aut, cre] , Manfred Beckmann [ctb], David Enot [ctb], Wanchang Lin [ctb] |
Maintainer: | Jasen Finch <[email protected]> |
License: | GPL (>= 3) |
Version: | 0.6.3 |
Built: | 2024-11-01 03:24:28 UTC |
Source: | https://github.com/aberhrml/metabodata |
Real world FIE-MS dataset.
data(abr1)
data(abr1)
FIE-MS data matrices developed from analysis of samples representing a time
course of pathogen attack in a model plant species (Brachypodium
distachyon). The data was developed in a single batch with all samples
randomised using a Thermo LTQ linear ion trap processed using
fiems_ltq_main
. Both positive and negative ion mode are given
(abr1$pos
and abr1$neg
). To avoid confusions, variable names
are given with a letter corresponding to the ionisation mode followed by the
actual nominal mass value (e.g. P130 corresponds to the nominal mass 130 in
the positive mode).
Experimental factors are given in the abr1$fact
data frame:
injorder:
sample injection order
name:
sample name
rep:
biological replicate for a given class
day:
number of days following infection after which the sample has been harvested
- Level H corresponds to an healthy plant.
class:
identical to
day except that class=6
when day=H
pathcdf,filecdf,name.org,remark:
are generated from profile
processing and are kept for traceability purposes.
Factor of interest for
classification are contained in abr1$fact$day
. There are 20
biological replicates in each class has
A list with the following elements:
fact |
A data frame containing experimental meta-data. |
pos |
A data frame for positive data with 120 observations and 2000 variables. |
neg |
A data frame for negative data with 120 observations and 2000 variables. |
Manfred Beckmann, David Enot and Wanchang Lin
The FIEmspro package https://github.com/aberHRML/FIEmspro
# Load data set data(abr1) # Select data set dat <- abr1$neg # number of observations and variables in the negative mode matrix dim(dat) # names of the variables dimnames(dat)[[2]] %>% head() # print out the experimental factors abr1$fact %>% head() # check out the repartition of class table(abr1$fact$class)
# Load data set data(abr1) # Select data set dat <- abr1$neg # number of observations and variables in the negative mode matrix dim(dat) # names of the variables dimnames(dat)[[2]] %>% head() # print out the experimental factors abr1$fact %>% head() # check out the repartition of class table(abr1$fact$class)
Displays available data sets.
availableDataSets(dataSetDir = "DataSets", internalDir = TRUE)
availableDataSets(dataSetDir = "DataSets", internalDir = TRUE)
dataSetDir |
directory containing local data set store. If |
internalDir |
stored the data set internally to the package installation location |
A tibble containing available data set information.
## Not run: availableDataSets() ## End(Not run)
## Not run: availableDataSets() ## End(Not run)
Display the available files for a given data set.
availableFiles(technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE)
availableFiles(technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE)
technique |
metabolomic technique name |
dataSet |
data set name |
dataSetDir |
directory containing local data set store. If |
internalDir |
stored the data set internally to the package installation location |
A tibble containing available file information.
## Not run: availableFiles('FIE-HRMS','BdistachyonTechnical') ## End(Not run)
## Not run: availableFiles('FIE-HRMS','BdistachyonTechnical') ## End(Not run)
Return a vector of available data sets for a given metabolomic technique.
dataSets(technique)
dataSets(technique)
technique |
metabolomic technique name |
A character vector of available data sets.
## Not run: dataSets(techniques()[1]) ## End(Not run)
## Not run: dataSets(techniques()[1]) ## End(Not run)
Return list containing experiment description elements
description( technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ... )
description( technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ... )
technique |
metabolomic technique name |
dataSet |
data set name |
dataSetDir |
directory to store local data sets. If |
internalDir |
Logical, should the directory for storing local data sets be internal to the package location. |
... |
arguments to pass to |
A list containing data set descriptors.
## Not run: description( techniques()[1], dataSets(techniques()[1])[1]) ## End(Not run)
## Not run: description( techniques()[1], dataSets(techniques()[1])[1]) ## End(Not run)
Download an example data set.
downloadDataSet( technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ask = TRUE, ... )
downloadDataSet( technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ask = TRUE, ... )
technique |
metabolomic technique name |
dataSet |
data set name |
dataSetDir |
directory to store local data sets. If |
internalDir |
stored the data set internally to the package installation location |
ask |
ask before downloading |
... |
arguments to pass to |
A list object containing the API request response results for the downloaded files.
## Not run: downloadDataSet('FIE-HRMS','BdistachyonTechnical') ## End(Not run)
## Not run: downloadDataSet('FIE-HRMS','BdistachyonTechnical') ## End(Not run)
Download specific files for a given example data set.
downloadFiles( files, technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ask = TRUE, ... )
downloadFiles( files, technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ask = TRUE, ... )
files |
character vector of file paths to download |
technique |
metabolomic technique name |
dataSet |
data set name |
dataSetDir |
directory to store local data sets. If |
internalDir |
stored the data set internally to the package installation location |
ask |
ask before downloading |
... |
arguments to pass to |
A list object containing the API request response results for the downloaded files.
## Not run: downloadFiles(c('31.mzML.gz','32.mzML.gz'),'FIE-HRMS','BdistachyonTechnical') ## End(Not run)
## Not run: downloadFiles(c('31.mzML.gz','32.mzML.gz'),'FIE-HRMS','BdistachyonTechnical') ## End(Not run)
Return a vector of file paths for a given data set of a given metabolomic technique.
filePaths(technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ...)
filePaths(technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ...)
technique |
metabolomic technique name |
dataSet |
data set name |
dataSetDir |
directory to store local data sets. If |
internalDir |
Logical, should the directory for storing local data sets be internal to the package location. |
... |
arguments to pass to |
A character vector of file paths.
## Not run: files <- filePaths( techniques()[1], dataSets(techniques()[1])[1]) head(files) ## End(Not run)
## Not run: files <- filePaths( techniques()[1], dataSets(techniques()[1])[1]) head(files) ## End(Not run)
Return tibble of run information for a given data set of a given metabolomics technique.
runinfo(technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ...)
runinfo(technique, dataSet, dataSetDir = "DataSets", internalDir = TRUE, ...)
technique |
metabolomic technique name |
dataSet |
data set name |
dataSetDir |
directory to store local data sets. If |
internalDir |
Logical, should the directory for storing local data sets be internal to the package location. |
... |
arguments to pass to |
A tibble containing sample information.
## Not run: info <- runinfo( techniques()[1], dataSets(techniques()[1])[1]) head(info) ## End(Not run)
## Not run: info <- runinfo( techniques()[1], dataSets(techniques()[1])[1]) head(info) ## End(Not run)
Return a vector of available metabolomic techniques.
techniques()
techniques()
A character vector of available techniques.
## Not run: techniques() ## End(Not run)
## Not run: techniques() ## End(Not run)