An R package containing example data sets for metabolomics analyses.
To install directly from this repository run:
remotes::install_github('aberHRML/metaboData',build_opts =c("--no-resave-data", "--no-manual"))
Or package can be installed via a drat repository hosted on github using:
install.packages('metaboData',repos = 'https://aberhrml.github.io/drat/')
Available data sets can be viewed using:
library(metaboData)
availableDataSets()
#>
#> FIE-HRMS
#> - BdistachyonEcotypes
#> - BdistachyonTechnical
#> - UrineTechnicalAvailable metabolomic techniques can be returned using:
techniques()
#> [1] "FIE-HRMS"Available data sets for a given metabolomic technique can be returned using:
dataSets(techniques()[1])
#> [1] "BdistachyonEcotypes" "BdistachyonTechnical" "UrineTechnical"File paths for data files within a given data set can be returned using:
files <- filePaths(
techniques()[1],
dataSets(techniques()[1])[1])
length(files)
#> [1] 68An experimental description can be retrieved for a given experiment of a given metabolomic technique using:
experimentDescription <- description(
techniques()[1],
dataSets(techniques()[1])[1])
str(experimentDescription)
#> List of 8
#> $ Name : chr "BdistachyonEcotypes"
#> $ Technique : chr "Flow-infusion electrospray ionisation-high resolution mass spectrometry (FIE-HRMS)"
#> $ Organism : chr "Brachypodium distachyon"
#> $ Tissue : chr "leaf"
#> $ Description : chr "Comparison of leaf tissue from 4 B. distachyon ecotypes."
#> $ Sample_collection: chr "B. distachyon plants were grown to 21 days old. The middle 4cm section of the 3rd leaf from the base of the pla"| __truncated__
#> $ Extracion : chr "Samples were milled for 30 seconds at 30Hz whilst frozen then 700ul extraction solvent added (chloroform:methan"| __truncated__
#> $ MS_analysis : chr "A QC sample was prepared by taking an equal volume from each sample. Samples were run in a randomised block ord"| __truncated__Run information can be retrieved for a given experiment of a given metabolomic technique using:
info <- runinfo(
techniques()[1],
dataSets(techniques()[1])[1])
head(info)
#> # A tibble: 6 x 7
#> fileOrder injOrder fileName batch block name class
#> <dbl> <dbl> <chr> <dbl> <dbl> <chr> <chr>
#> 1 1 64 1.mzML.gz 1 5 ABR1_1 ABR1
#> 2 2 40 10.mzML.gz 1 3 ABR1_10 ABR1
#> 3 3 52 11.mzML.gz 1 4 ABR1_11 ABR1
#> 4 4 67 12.mzML.gz 1 5 ABR1_12 ABR1
#> 5 5 32 13.mzML.gz 1 3 ABR1_13 ABR1
#> 6 6 53 14.mzML.gz 1 4 ABR1_14 ABR1The abr1 FIE-MS data set is included from the
FIEmspro package.