MAIT_identify_metabolites
MAIT metabolite identification
Apply function to variables
Apply function to samples
Aggregate samples
Background correction
Baseline correction
Apply by groups
Apply by group
absorbance_to_transmittance
Convert absorbance to transmittance
Boxplot of variables
Convert CHEBI codes to KEGG codes.
Convert from ChemoSpec
Convert HMDB codes to KEGG codes.
Correlations test
convert_keggpathway_2_reactiongraph
Convert KEGGPathway object to graph object.
Count missing values
Analysis of variance
compare_regions_by_sample
Compare regions by sample
Perform cluster analysis
detect_nmr_peaks_from_dataset
Detection of the peaks in an NMR spectra dataset.
Correlation test of two variables or samples
Dataset from peaks
Data correction
Dataset correlations
Check dataset
create_pathway_with_reactions
Creates the pathway, with reactions included in the nodes.
convert_multiple_spcmnm_to_kegg
Convert specmine metabolite codes to KEGG codes.
Check 2D dataset.
count_missing_values_per_sample
Count missing values per sample
Flat pattern filter
First derivative
Cubic root transformation
Convert metadata to factor
Boxplot of variables with metadata's variable factors
Perform feature selection
Get all organisms in KEGG.
Returns an object of KEGGPathway of the pathway especified in pathcode.
Get x-axis values as numbers
Get metadata
get_metabolights_study_samples_files
Get list of files from an assay of the MetaboLights study and saves it in a csv file.
Get x-axis label
Impute missing values with KNN
get_metabolights_study_metadata_assay
Download metadata file from an assay of MetaboLights study
Impute missing values with linear approximation
get_metabolights_study_files_assay
Download data files from an assay of MetaboLights study
count_missing_values_per_variable
Count missing values per variable
Correlations heatmap
Perform hierarchical clustering analysis
Get sample names
Create dataset
Create 2D dataset
Plot dendrogram
Get data
Plot dendrogram
Get data value
Get data as data frame
Download MetaboLights study files.
Get the metabolic pathways present in given organism.
Impute missing values with mean
Impute missing values with median
metabolights_studies_list
List the study IDs available in the MetaboLights database.
Kolmogorov-Smirnov tests on dataset
Normalize data
Metadata as variables
Kruskal-Wallis tests on dataset
Normalize samples
Get the names of the compounds that correspond to the kegg codes given.
Detection of the peaks in an 2D NMR spectra dataset.
Perform selection by filter
Get data
Get data values
Plot Kruskal-Wallis tests results
Peaks per sample
Plot Kolmogorov-Smirnov tests results
Get list of files per assay for MetaboLights study.
Import for Thermo Galactic's spc file format
These functions allow to import .spc files.
Remove data variables
Predict samples
remove_metadata_variables
Remove metadata's variables
PCA biplot
NMR metabolite identification
Logarithmic transformation.
Linear regression on one variable
PCA analysis (classical)
Multiplot
Get metadata value
Low level fusion
Show cluster's members
Plot kmeans clusters
Subset x-values
Get metadata variable
Mean centering
subset_x_values_by_interval
Subset x-values by interval
Find equal samples
Fold change applied on two variables
Fold change analysis
PCA k-means pairs plot
3D PCA scores plot
PCA pairs plot
Read data from (J)DX files
Read data from SPC files
Values per peak
Get sample's names from SPC files
2D PCA scores plot
Get x-axis values as text
recursive_feature_elimination
Perform recursive feature elimination
Get sample's names from DX files
Variables as metadata
Get value label
Impute missing values with value replacement
indexes_to_xvalue_interval
Get the x-values of a vector of indexes
Get only the paths of the organism that contain one or more of the given compounds.
Get type of data
Linear Regression
Group peaks
Get peak values
3D pca plot
Linear regression p-values table
Linear regression r-squared
Linear regression coefficient table
Multifactor ANOVA
Multi Class Summary
Multiplicative scatter correction
Remove data
Missing values imputation
Get number of samples
Get number of x values
3D PCA biplot (interactive)
PCA analysis (robust)
3D PCA scores plot (interactive)
PCA scree plot
PCA importance
Perform k-means clustering analysis
Merge data and metadata
Check type of data
Plot of 2D spectra
Creates the metabolic pathway wanted. If any of the given compounds is present in the pathway, it is coloured differently.
Offset correction
read_varian_2dspectra_raw
Function that reads raw 2D spectra (intensity over time spectra) from the varian format and processes them to ppm spectra.
Function that reads raw spectra (intensity over time spectra) from the varian format and processes them to ppm spectra.
Peaks per samples
Plot fold change results
Plot ANOVA results
Merge two datasets
Replace data value
remove_x_values_by_interval
Remove x-values by interval
Set new x-values
multifactor_aov_varexp_table
Multifactor ANOVA variability explained table
3D PCA k-means plot (interactive)
multifactor_aov_pvalues_table
Multifactor ANOVA p-values table
2D PCA k-means plot
Plot the peaks of a MS or NMR dataset.
Plot t-tests results
Statistics of variables
t-Tests on dataset
Summary of variables importance
Shift correction
subset_by_samples_and_xvalues
Subset by samples and x-values
Plot variable distribution on two factors
plot_regression_coefs_pvalues
Plot regression coefficient and p-values
Volcano plot
Get x-values indexes
Read dataset from CSV
Replace metadata's value
Savitzky-golay transformation
Plot spectra
Set x-label
Subset metadata
Set value label
Read CSVs from folder
Remove samples
2D Dataset summary
remove_samples_by_na_metadata
Remove samples by NA on metadata
Read Bruker processed spectra.
Subset random samples
Read CSV data
Plot spectra (simple)
Smoothing interpolation
Read dataset from (J)DX files
Standard Normal Variate
Remove samples by NAs
Read dataset from SPC files
Remove variables by NAs
Read metadata
Set samples names
Set new metadata
Subset samples
Dataset summary
Remove interval of peaks
Read Bruker processed 2D spectra.
Read MS spectra
Read multiple CSVs
Train models
Transform data
remove_peaks_interval_sample_list
Remove interval of peaks (sample list)
subset_samples_by_metadata_values
Subset samples by metadata values
Scale dataset
Information on the library of NMR reference spectra in our package.
Train and predict
Statistics of samples
Scale data matrix
Train classifier
transmittance_to_absorbance
Convert transmittance to absorbance
Values per peak
xvalue_interval_to_indexes
Get indexes of an interval of x-values