Metabolomics and Spectral Data Analysis and Mining


[Up] [Top]

Documentation for package ‘specmine’ version 3.1.6

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 --

check_2d_dataset Check 2D dataset.
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_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
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_2d_dataset Create 2D dataset
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_2d_data Get data
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
peak_detection2d Detection of the peaks in an 2D NMR spectra dataset.
plotvar_twofactor Plot variable distribution on two factors
plot_2d_spectra Plot of 2D spectra
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

-- R --

read_Bruker_files Read Bruker processed spectra.
read_Bruker_files_2d Read Bruker processed 2D 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_2dspectra_raw Function that reads raw 2D spectra (intensity over time spectra) from the varian format and processes them to ppm spectra.
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_2d_dataset 2D Dataset summary
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