# Metabolomics and Spectral Data Analysis and Mining

## Documentation for package ‘specmine’ version 3.0.1

- DESCRIPTION file.

## Help Pages

A B C D F G H I K L M N O P R S T V X

## -- A --

absorbance_to_transmittance | Convert absorbance to transmittance
aggregate_samples | Aggregate samples
aov_all_vars | Analysis of variance
apply_by_group | Apply by group
apply_by_groups | Apply by groups
apply_by_sample | Apply function to samples
apply_by_variable | Apply function to variables

## -- B --

background_correction | Background correction
baseline_correction | Baseline correction
boxplot_variables | Boxplot of variables
boxplot_vars_factor | Boxplot of variables with metadata's variable factors

## -- C --

cachexia | Human Cachexia data
check_dataset | Check dataset
clustering | Perform cluster analysis
compare_regions_by_sample | Compare regions by sample
convert_chebi_to_kegg | Convert CHEBI codes to KEGG codes.
convert_from_chemospec | Convert from ChemoSpec
convert_from_hyperspec | Convert from hyperspec
convert_hmdb_to_kegg | Convert HMDB codes to KEGG codes.
convert_keggpathway_2_reactiongraph | Convert KEGGPathway object to graph object.
convert_multiple_spcmnm_to_kegg | Convert specmine metabolite codes to KEGG codes.
convert_to_factor | Convert metadata to factor
convert_to_hyperspec | Convert to hyperspec
correlations_dataset | Dataset correlations
correlations_test | Correlations test
correlation_test | Correlation test of two variables or samples
count_missing_values | Count missing values
count_missing_values_per_sample | Count missing values per sample
count_missing_values_per_variable | Count missing values per variable
create_dataset | Create dataset
create_pathway_with_reactions | Creates the pathway, with reactions included in the nodes.
cubic_root_transform | Cubic root transformation

## -- D --

dataset_from_peaks | Dataset from peaks
data_correction | Data correction
dendrogram_plot | Plot dendrogram
dendrogram_plot_col | Plot dendrogram
detect_nmr_peaks_from_dataset | Detection of the peaks in an NMR spectra dataset.

## -- F --

feature_selection | Perform feature selection
filter_feature_selection | Perform selection by filter
find_equal_samples | Find equal samples
first_derivative | First derivative
flat_pattern_filter | Flat pattern filter
fold_change | Fold change analysis
fold_change_var | Fold change applied on two variables

## -- G --

get_cpd_names | Get the names of the compounds that correspond to the kegg codes given.
get_data | Get data
get_data_as_df | Get data as data frame
get_data_value | Get data value
get_data_values | Get data values
get_files_list_per_assay | Get list of files per assay for MetaboLights study.
get_metabolights_study | Download MetaboLights study files.
get_metabolights_study_files_assay | Download data files from an assay of MetaboLights study
get_metabolights_study_metadata_assay | Download metadata file from an assay of MetaboLights study
get_metabolights_study_samples_files | Get list of files from an assay of the MetaboLights study and saves it in a csv file.
get_MetabolitePath | Returns an object of KEGGPathway of the pathway especified in pathcode.
get_metabPaths_org | Get the metabolic pathways present in given organism.
get_metadata | Get metadata
get_metadata_value | Get metadata value
get_metadata_var | Get metadata variable
get_OrganismsCodes | Get all organisms in KEGG.
get_paths_with_cpds_org | Get only the paths of the organism that contain one or more of the given compounds.
get_peak_values | Get peak values
get_samples_names_dx | Get sample's names from DX files
get_samples_names_spc | Get sample's names from SPC files
get_sample_names | Get sample names
get_type | Get type of data
get_value_label | Get value label
get_x_label | Get x-axis label
get_x_values_as_num | Get x-axis values as numbers
get_x_values_as_text | Get x-axis values as text
group_peaks | Group peaks

## -- H --

heatmap_correlations | Correlations heatmap
hierarchical_clustering | Perform hierarchical clustering analysis

## -- I --

impute_nas_knn | Impute missing values with KNN
impute_nas_linapprox | Impute missing values with linear approximation
impute_nas_mean | Impute missing values with mean
impute_nas_median | Impute missing values with median
impute_nas_value | Impute missing values with value replacement
indexes_to_xvalue_interval | Get the x-values of a vector of indexes
is_spectra | Check type of data

## -- K --

kmeans_clustering | Perform k-means clustering analysis
kmeans_plot | Plot kmeans clusters
kmeans_result_df | Show cluster's members
kruskalTest_dataset | Kruskal-Wallis tests on dataset
ksTest_dataset | Kolmogorov-Smirnov tests on dataset

## -- L --

linregression_onevar | Linear regression on one variable
linreg_all_vars | Linear Regression
linreg_coef_table | Linear regression coefficient table
linreg_pvalue_table | Linear regression p-values table
linreg_rsquared | Linear regression r-squared
log_transform | Logarithmic transformation.
low_level_fusion | Low level fusion

## -- M --

MAIT_identify_metabolites | MAIT metabolite identification
mean_centering | Mean centering
merge_datasets | Merge two datasets
merge_data_metadata | Merge data and metadata
metabolights_studies_list | List the study IDs available in the MetaboLights database.
metadata_as_variables | Metadata as variables
missingvalues_imputation | Missing values imputation
msc_correction | Multiplicative scatter correction
multiClassSummary | Multi Class Summary
multifactor_aov_all_vars | Multifactor ANOVA
multifactor_aov_pvalues_table | Multifactor ANOVA p-values table
multifactor_aov_varexp_table | Multifactor ANOVA variability explained table
multiplot | Multiplot

## -- N --

nmr_identification | NMR metabolite identification
normalize | Normalize data
normalize_samples | Normalize samples
num_samples | Get number of samples
num_x_values | Get number of x values

## -- O --

offset_correction | Offset correction

## -- P --

pathway_analysis | Creates the metabolic pathway wanted. If any of the given compounds is present in the pathway, it is coloured differently.
pca_analysis_dataset | PCA analysis (classical)
pca_biplot | PCA biplot
pca_biplot3D | 3D PCA biplot (interactive)
pca_importance | PCA importance
pca_kmeans_plot2D | 2D PCA k-means plot
pca_kmeans_plot3D | 3D PCA k-means plot (interactive)
pca_pairs_kmeans_plot | PCA k-means pairs plot
pca_pairs_plot | PCA pairs plot
pca_plot_3d | 3D pca plot
pca_robust | PCA analysis (robust)
pca_scoresplot2D | 2D PCA scores plot
pca_scoresplot3D | 3D PCA scores plot
pca_scoresplot3D_rgl | 3D PCA scores plot (interactive)
pca_screeplot | PCA scree plot
peaks_per_sample | Peaks per sample
peaks_per_samples | Peaks per samples
plotvar_twofactor | Plot variable distribution on two factors
plot_anova | Plot ANOVA results
plot_fold_change | Plot fold change results
plot_kruskaltest | Plot Kruskal-Wallis tests results
plot_kstest | Plot Kolmogorov-Smirnov tests results
plot_peaks | Plot the peaks of a MS or NMR dataset.
plot_regression_coefs_pvalues | Plot regression coefficient and p-values
plot_spectra | Plot spectra
plot_spectra_simple | Plot spectra (simple)
plot_ttests | Plot t-tests results
predict_samples | Predict samples
propolis | Brazilian Propolis from different Harvest Seasons and different Agroecological Regions (dataset)
propolisSampleList | Brazilian Propolis from different Harvest Seasons and different Agroecological Regions (sample list)

## -- R --

read_Bruker_files | Read Bruker processed spectra.
read_csvs_folder | Read CSVs from folder
read_dataset_csv | Read dataset from CSV
read_dataset_dx | Read dataset from (J)DX files
read_dataset_spc | Read dataset from SPC files
read_data_csv | Read CSV data
read_data_dx | Read data from (J)DX files
read_data_spc | Read data from SPC files
read_metadata | Read metadata
read_ms_spectra | Read MS spectra
read_multiple_csvs | Read multiple CSVs
read_spc_nosubhdr | Import for Thermo Galactic's spc file format These functions allow to import .spc files.
read_varian_spectra_raw | Function that reads raw spectra (intensity over time spectra) from the varian format and processes them to ppm spectra.
recursive_feature_elimination | Perform recursive feature elimination
remove_data | Remove data
remove_data_variables | Remove data variables
remove_metadata_variables | Remove metadata's variables
remove_peaks_interval | Remove interval of peaks
remove_peaks_interval_sample_list | Remove interval of peaks (sample list)
remove_samples | Remove samples
remove_samples_by_nas | Remove samples by NAs
remove_samples_by_na_metadata | Remove samples by NA on metadata
remove_variables_by_nas | Remove variables by NAs
remove_x_values_by_interval | Remove x-values by interval
replace_data_value | Replace data value
replace_metadata_value | Replace metadata's value

## -- S --

savitzky_golay | Savitzky-golay transformation
scaling | Scale dataset
scaling_samples | Scale data matrix
set_metadata | Set new metadata
set_sample_names | Set samples names
set_value_label | Set value label
set_x_label | Set x-label
set_x_values | Set new x-values
shift_correction | Shift correction
smoothing_interpolation | Smoothing interpolation
snv_dataset | Standard Normal Variate
spectra_options | Information on the library of NMR reference spectra in our package.
stats_by_sample | Statistics of samples
stats_by_variable | Statistics of variables
subset_by_samples_and_xvalues | Subset by samples and x-values
subset_metadata | Subset metadata
subset_random_samples | Subset random samples
subset_samples | Subset samples
subset_samples_by_metadata_values | Subset samples by metadata values
subset_x_values | Subset x-values
subset_x_values_by_interval | Subset x-values by interval
summary_var_importance | Summary of variables importance
sum_dataset | Dataset summary

## -- T --

train_and_predict | Train and predict
train_classifier | Train classifier
train_models_performance | Train models
transform_data | Transform data
transmittance_to_absorbance | Convert transmittance to absorbance
tTests_dataset | t-Tests on dataset

## -- V --

values_per_peak | Values per peak
values_per_sample | Values per peak
variables_as_metadata | Variables as metadata
volcano_plot_fc_tt | Volcano plot

## -- X --

xvalue_interval_to_indexes | Get indexes of an interval of x-values
x_values_to_indexes | Get x-values indexes