API for specmine
Metabolomics and Spectral Data Analysis and Mining

Global functions
.spc.ylab Source code
MAIT_identify_metabolites Man page Source code
absorbance_to_transmittance Man page Source code
aggregate_samples Man page
aov_all_vars Man page
apply_by_group Man page
apply_by_groups Man page
apply_by_sample Man page
apply_by_variable Man page
background_correction Man page Source code
baseline_correction Man page Source code
boxplot_variables Man page
boxplot_vars_factor Man page Source code
cachexia Man page
calculate_ellipses Source code
cassavaPPD Man page
check_dataset Man page
choose_nmr_references Man page Source code
clustering Man page Source code
compare_regions_by_sample Man page
conversion_table Man page
convert_from_chemospec Man page Source code
convert_from_hyperspec Man page Source code
convert_hmdb_to_kegg Man page Source code
convert_keggpathway_2_reactiongraph Man page Source code
convert_to_factor Man page
convert_to_hyperspec Man page Source code
correlation_test Man page Source code
correlations_dataset Man page Source code
correlations_test Man page Source code
count_missing_values Man page
count_missing_values_per_sample Man page
count_missing_values_per_variable Man page
create_dataset Man page
create_metaboanalyst_mat Source code
create_pathway_with_reactions Man page Source code
cubic_root_transform Man page
data_correction Man page
dataset_from_peaks Man page
dendrogram_plot Man page
dendrogram_plot_col Man page
descendMin Source code
detect_nmr_peaks Source code
detect_nmr_peaks_from_dataset Man page Source code
feature_selection Man page Source code
filter_feature_selection Man page Source code
findEqualGreaterM Source code
find_corr Man page Source code
find_equal_samples Man page
first_derivative Man page Source code
flat_pattern_filter Man page
fold_change Man page Source code
fold_change_var Man page Source code
get_MetabolitePath Man page Source code
get_OrganismsCodes Man page Source code
get_cpd_names Man page Source code
get_data Man page
get_data_as_df Man page
get_data_value Man page
get_data_values Man page
get_hmdbs_with_specs_id Man page Source code
get_metabPaths_org Man page Source code
get_metabolights_study Man page Source code
get_metabolights_study_list Man page Source code
get_metadata Man page
get_metadata_value Man page
get_metadata_var Man page
get_paths_with_cpds_org Man page Source code
get_peak_values Man page
get_sample_names Man page
get_samples_names_dx Man page
get_samples_names_spc Man page Source code
get_type Man page
get_value_label Man page
get_x_label Man page
get_x_values_as_num Man page
get_x_values_as_text Man page
group_peaks Man page
group_peaks_metaboanalyst Source code
heatmap_correlations Man page Source code
hierarchical_clustering Man page Source code
impute_nas_knn Man page
impute_nas_linapprox Man page Source code
impute_nas_mean Man page
impute_nas_median Man page
impute_nas_value Man page
indexes_to_xvalue_interval Man page
is_spectra Man page
is_windows Source code Source code
jaccard_index Man page Source code
kmeans_clustering Man page Source code
kmeans_plot Man page Source code
kmeans_result_df Man page Source code
kruskalTest_dataset Man page Source code
ksTest_dataset Man page Source code
linreg_all_vars Man page
linreg_coef_table Man page Source code
linreg_pvalue_table Man page Source code
linreg_rsquared Man page Source code
linregression_onevar Man page
log_transform Man page
low_level_fusion Man page
maps_con Man page
mean_centering Man page Source code
merge_data_metadata Man page
merge_datasets Man page
metadata_as_variables Man page Source code
missingvalues_imputation Man page
ms_create_matrix Source code
ms_fill_peaks Source code
ms_rt_correction Source code
msc_correction Man page
multiClassSummary Man page
multifactor_aov_all_vars Man page
multifactor_aov_pvalues_table Man page Source code
multifactor_aov_varexp_table Man page Source code
multiplot Man page Source code
nmr_1d_spectra Man page
nmr_1d_spectra_options Man page
nmr_clustering Man page Source code
nmr_identification Man page Source code
normalize Man page
normalize_samples Man page
num_samples Man page
num_x_values Man page
offset_correction Man page Source code
pathway_analysis Man page Source code
pca_analysis_dataset Man page Source code
pca_biplot Man page Source code
pca_biplot3D Man page Source code
pca_importance Man page Source code
pca_kmeans_plot2D Man page Source code
pca_kmeans_plot3D Man page Source code
pca_pairs_kmeans_plot Man page Source code
pca_pairs_plot Man page Source code
pca_plot_3d Man page
pca_robust Man page Source code
pca_scoresplot2D Man page Source code
pca_scoresplot3D Man page Source code
pca_scoresplot3D_rgl Man page Source code
pca_screeplot Man page Source code
peaks_per_sample Man page
peaks_per_samples Man page
plot_anova Man page Source code
plot_fold_change Man page Source code
plot_kruskaltest Man page Source code
plot_kstest Man page Source code
plot_peaks Man page Source code
plot_regression_coefs_pvalues Man page Source code
plot_spectra Man page
plot_spectra_simple Man page
plot_ttests Man page Source code
plotvar_twofactor Man page Source code
predict_samples Man page Source code
propolis Man page
propolisSampleList Man page
readBruker Source code
read_Bruker_files Man page Source code
read_csvs_folder Man page
read_data_csv Man page
read_data_dx Man page
read_data_spc Man page
read_dataset_csv Man page
read_dataset_dx Man page
read_dataset_spc Man page
read_metadata Man page
read_ms_spec Source code
read_ms_spectra Man page Source code
read_multiple_csvs Man page
read_spc_nosubhdr Man page
read_varian_spectra_raw Man page Source code
read_varian_spectrum_raw Source code
rectUnique Source code
recursive_feature_elimination Man page Source code
remove_data Man page
remove_data_variables Man page
remove_metadata_variables Man page
remove_peaks_interval Man page
remove_peaks_interval_sample_list Man page
remove_samples Man page
remove_samples_by_na_metadata Man page
remove_samples_by_nas Man page
remove_variables_by_nas Man page
remove_x_values_by_interval Man page
replace_data_value Man page
replace_metadata_value Man page
savitzky_golay Man page Source code
scale_to_interval Source code
scaling Man page
scaling_samples Man page
set_groups_metaboanalyst Source code
set_metadata Man page
set_sample_names Man page
set_value_label Man page
set_x_label Man page
set_x_values Man page
shift_correction Man page
smoothing_interpolation Man page Source code
smoothing_spcbin_hyperspec Source code
smoothing_spcloess_hyperspec Source code
snv_dataset Man page Source code
spinalCord Man page
stats_by_sample Man page
stats_by_variable Man page
subset_by_samples_and_xvalues Man page
subset_metadata Man page
subset_random_samples Man page
subset_samples Man page
subset_samples_by_metadata_values Man page
subset_x_values Man page
subset_x_values_by_interval Man page
sum_dataset Man page
summary_var_importance Man page Source code
tTests_dataset Man page Source code
tTests_pvalue Source code
trainClassifier Source code
train_and_predict Man page Source code
train_classifier Man page Source code
train_models_performance Man page Source code
transform_data Man page
transmittance_to_absorbance Man page Source code
trim Source code
values_per_peak Man page
values_per_sample Man page
var_importance Source code
variables_as_metadata Man page Source code
volcano_plot_fc_tt Man page Source code
x_values_to_indexes Man page
xvalue_interval_to_indexes Man page
specmine documentation built on May 2, 2019, 3:10 a.m.