Man pages for specmine
Metabolomics and Spectral Data Analysis and Mining

absorbance_to_transmittanceConvert absorbance to transmittance
aggregate_samplesAggregate samples
aov_all_varsAnalysis of variance
apply_by_groupApply by group
apply_by_groupsApply by groups
apply_by_sampleApply function to samples
apply_by_variableApply function to variables
background_correctionBackground correction
baseline_correctionBaseline correction
boxplot_variablesBoxplot of variables
boxplot_vars_factorBoxplot of variables with metadata's variable factors
cachexiaHuman Cachexia data
cassavaPPDCassava Postharvest Physiological Deterioration
check_datasetCheck dataset
choose_nmr_referencesChoose the metabolites' spectra to be the reference.
clusteringPerform cluster analysis
compare_regions_by_sampleCompare regions by sample
conversion_tableConversion table.
convert_from_chemospecConvert from ChemoSpec
convert_from_hyperspecConvert from hyperspec
convert_hmdb_to_keggConvert HMDB codes to KEGG codes.
convert_keggpathway_2_reactiongraphConvert KEGGPathway object to graph object.
convert_to_factorConvert metadata to factor
convert_to_hyperspecConvert to hyperspec
correlations_datasetDataset correlations
correlations_testCorrelations test
correlation_testCorrelation test of two variables or samples
count_missing_valuesCount missing values
count_missing_values_per_sampleCount missing values per sample
count_missing_values_per_variableCount missing values per variable
create_datasetCreate dataset
create_pathway_with_reactionsCreates the pathway, with reactions included in the nodes.
cubic_root_transformCubic root transformation
data_correctionData correction
dataset_from_peaksDataset from peaks
dendrogram_plotPlot dendrogram
dendrogram_plot_colPlot dendrogram
detect_nmr_peaks_from_datasetDetection of the peaks in an NMR spectra dataset.
feature_selectionPerform feature selection
filter_feature_selectionPerform selection by filter
find_corrFind the best correlation value for the clustering of peaks
find_equal_samplesFind equal samples
first_derivativeFirst derivative
flat_pattern_filterFlat pattern filter
fold_changeFold change analysis
fold_change_varFold change applied on two variables
get_cpd_namesGet the names of the compounds that correspond to the kegg...
get_dataGet data
get_data_as_dfGet data as data frame
get_data_valueGet data value
get_data_valuesGet data values
get_hmdbs_with_specs_idHMDB code and name of HMDB 1d-NMR spectra.
get_metabolights_studyDownload Metabolights study files.
get_metabolights_study_listList of metabolights studies available to download.
get_MetabolitePathReturns an object of KEGGPathway of the pathway especified in...
get_metabPaths_orgGet the metabolic pathways present in given organism.
get_metadataGet metadata
get_metadata_valueGet metadata value
get_metadata_varGet metadata variable
get_OrganismsCodesGet all organisms in KEGG.
get_paths_with_cpds_orgGet only the paths of the organism that contain one or more...
get_peak_valuesGet peak values
get_sample_namesGet sample names
get_samples_names_dxGet sample's names from DX files
get_samples_names_spcGet sample's names from SPC files
get_typeGet type of data
get_value_labelGet value label
get_x_labelGet x-axis label
get_x_values_as_numGet x-axis values as numbers
get_x_values_as_textGet x-axis values as text
group_peaksGroup peaks
heatmap_correlationsCorrelations heatmap
hierarchical_clusteringPerform hierarchical clustering analysis
impute_nas_knnImpute missing values with KNN
impute_nas_linapproxImpute missing values with linear approximation
impute_nas_meanImpute missing values with mean
impute_nas_medianImpute missing values with median
impute_nas_valueImpute missing values with value replacement
indexes_to_xvalue_intervalGet the x-values of a vector of indexes
is_spectraCheck type of data
jaccard_indexJaccard Index
kmeans_clusteringPerform k-means clustering analysis
kmeans_plotPlot kmeans clusters
kmeans_result_dfShow cluster's members
kruskalTest_datasetKruskal-Wallis tests on dataset
ksTest_datasetKolmogorov-Smirnov tests on dataset
linreg_all_varsLinear Regression
linreg_coef_tableLinear regression coefficient table
linreg_pvalue_tableLinear regression p-values table
linregression_onevarLinear regression on one variable
linreg_rsquaredLinear regression r-squared
log_transformLogarithmic transformation.
low_level_fusionLow level fusion
MAIT_identify_metabolitesMAIT metabolite identification
maps_conData frame with the connections between the metabolic...
mean_centeringMean centering
merge_data_metadataMerge data and metadata
merge_datasetsMerge two datasets
metadata_as_variablesMetadata as variables
missingvalues_imputationMissing values imputation
msc_correctionMultiplicative scatter correction
multiClassSummaryMulti Class Summary
multifactor_aov_all_varsMultifactor ANOVA
multifactor_aov_pvalues_tableMultifactor ANOVA p-values table
multifactor_aov_varexp_tableMultifactor ANOVA variability explained table
multiplotMultiplot
nmr_1d_spectraList of reference 1D-NMR peak lists.
nmr_1d_spectra_optionsConditions of acquirement of the different refernece peak...
nmr_clusteringCluster of variables (peaks) in a NMR peaks dataset for...
nmr_identificationFunction to do NMR metabolite identification
normalizeNormalize data
normalize_samplesNormalize samples
num_samplesGet number of samples
num_x_valuesGet number of x values
offset_correctionOffset correction
pathway_analysisCreates the metabolic pathway wanted. If any of the given...
pca_analysis_datasetPCA analysis (classical)
pca_biplotPCA biplot
pca_biplot3D3D PCA biplot (interactive)
pca_importancePCA importance
pca_kmeans_plot2D2D PCA k-means plot
pca_kmeans_plot3D3D PCA k-means plot (interactive)
pca_pairs_kmeans_plotPCA k-means pairs plot
pca_pairs_plotPCA pairs plot
pca_plot_3d3D pca plot
pca_robustPCA analysis (robust)
pca_scoresplot2D2D PCA scores plot
pca_scoresplot3D3D PCA scores plot
pca_scoresplot3D_rgl3D PCA scores plot (interactive)
pca_screeplotPCA scree plot
peaks_per_samplePeaks per sample
peaks_per_samplesPeaks per samples
plot_anovaPlot ANOVA results
plot_fold_changePlot fold change results
plot_kruskaltestPlot Kruskal-Wallis tests results
plot_kstestPlot Kolmogorov-Smirnov tests results
plot_peaksPlot the peaks of a MS or NMR dataset.
plot_regression_coefs_pvaluesPlot regression coefficient and p-values
plot_spectraPlot spectra
plot_spectra_simplePlot spectra (simple)
plot_ttestsPlot t-tests results
plotvar_twofactorPlot variable distribution on two factors
predict_samplesPredict samples
propolisBrazilian Propolis from different Harvest Seasons and...
propolisSampleListBrazilian Propolis from different Harvest Seasons and...
read_Bruker_filesRead Bruker processed spectra.
read_csvs_folderRead CSVs from folder
read_data_csvRead CSV data
read_data_dxRead data from (J)DX files
read_dataset_csvRead dataset from CSV
read_dataset_dxRead dataset from (J)DX files
read_dataset_spcRead dataset from SPC files
read_data_spcRead data from SPC files
read_metadataRead metadata
read_ms_spectraRead MS spectra
read_multiple_csvsRead multiple CSVs
read-spcImport for Thermo Galactic's spc file format These functions...
read_varian_spectra_rawFunction that reads raw spectra (intensity over time spectra)...
recursive_feature_eliminationPerform recursive feature elimination
remove_dataRemove data
remove_data_variablesRemove data variables
remove_metadata_variablesRemove metadata's variables
remove_peaks_intervalRemove interval of peaks
remove_peaks_interval_sample_listRemove interval of peaks (sample list)
remove_samplesRemove samples
remove_samples_by_na_metadataRemove samples by NA on metadata
remove_samples_by_nasRemove samples by NAs
remove_variables_by_nasRemove variables by NAs
remove_x_values_by_intervalRemove x-values by interval
replace_data_valueReplace data value
replace_metadata_valueReplace metadata's value
savitzky_golaySavitzky-golay transformation
scalingScale dataset
scaling_samplesScale data matrix
set_metadataSet new metadata
set_sample_namesSet samples names
set_value_labelSet value label
set_x_labelSet x-label
set_x_valuesSet new x-values
shift_correctionShift correction
smoothing_interpolationSmoothing interpolation
snv_datasetStandard Normal Variate
spinalCordBrazilian Propolis from different Harvest Seasons and...
stats_by_sampleStatistics of samples
stats_by_variableStatistics of variables
subset_by_samples_and_xvaluesSubset by samples and x-values
subset_metadataSubset metadata
subset_random_samplesSubset random samples
subset_samplesSubset samples
subset_samples_by_metadata_valuesSubset samples by metadata values
subset_x_valuesSubset x-values
subset_x_values_by_intervalSubset x-values by interval
sum_datasetDataset summary
summary_var_importanceSummary of variables importance
train_and_predictTrain and predict
train_classifierTrain classifier
train_models_performanceTrain models
transform_dataTransform data
transmittance_to_absorbanceConvert transmittance to absorbance
tTests_datasett-Tests on dataset
values_per_peakValues per peak
values_per_sampleValues per peak
variables_as_metadataVariables as metadata
volcano_plot_fc_ttVolcano plot
xvalue_interval_to_indexesGet indexes of an interval of x-values
x_values_to_indexesGet x-values indexes
specmine documentation built on May 2, 2019, 3:10 a.m.