specmine: Metabolomics and Spectral Data Analysis and Mining

Provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning and feature selection. Case studies can be found on the website: http://darwin.di.uminho.pt/metabolomics .

AuthorChristopher Costa <chrisbcl@hotmail.com>, Marcelo Maraschin <mtocsy@gmail.com>, Miguel Rocha <mrocha@di.uminho.pt>
Date of publication2015-11-10 11:08:16
MaintainerChristopher Costa <chrisbcl@hotmail.com>
LicenseGPL (>= 2)
Version1.0

View on CRAN

Man pages

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

background_correction: Background correction

baseline_correction: Baseline correction

boxplot_variables: Boxplot of variables

boxplot_vars_factor: Boxplot of variables with metadata's variable factors

cachexia: Human Cachexia data

cassavaPPD: Cassava Postharvest Physiological Deterioration

check_dataset: Check dataset

clustering: Perform cluster analysis

compare_regions_by_sample: Compare regions by sample

convert_from_chemospec: Convert from ChemoSpec

convert_from_hyperspec: Convert from hyperspec

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

cubic_root_transform: Cubic root transformation

data_correction: Data correction

dataset_from_peaks: Dataset from peaks

dendrogram_plot: Plot dendrogram

dendrogram_plot_col: Plot dendrogram

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

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_metadata: Get metadata

get_metadata_value: Get metadata value

get_metadata_var: Get metadata variable

get_peak_values: Get peak values

get_sample_names: Get sample names

get_samples_names_dx: Get sample's names from DX files

get_samples_names_spc: Get sample's names from SPC files

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

heatmap_correlations: Correlations heatmap

hierarchical_clustering: Perform hierarchical clustering analysis

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

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

linreg_all_vars: Linear Regression

linreg_coef_table: Linear regression coefficient table

linreg_pvalue_table: Linear regression p-values table

linregression_onevar: Linear regression on one variable

linreg_rsquared: Linear regression r-squared

log_transform: Logarithmic transformation.

low_level_fusion: Low level fusion

MAIT_identify_metabolites: MAIT metabolite identification

mean_centering: Mean centering

merge_data_metadata: Merge data and metadata

merge_datasets: Merge two datasets

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

normalize: Normalize data

normalize_samples: Normalize samples

num_samples: Get number of samples

num_x_values: Get number of x values

offset_correction: Offset correction

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

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_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

plotvar_twofactor: Plot variable distribution on two factors

predict_samples: Predict samples

propolis: Brazilian Propolis from different Harvest Seasons and...

propolisSampleList: Brazilian Propolis from different Harvest Seasons and...

read_csvs_folder: Read CSVs from folder

read_data_csv: Read CSV data

read_data_dx: Read data from (J)DX files

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_spc: Read data from SPC files

read_metadata: Read metadata

read_ms_spectra: Read MS spectra

read_multiple_csvs: Read multiple CSVs

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_na_metadata: Remove samples by NA on metadata

remove_samples_by_nas: Remove samples by NAs

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

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

spinalCord: Brazilian Propolis from different Harvest Seasons and...

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

sum_dataset: Dataset summary

summary_var_importance: Summary of variables importance

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

values_per_peak: Values per peak

values_per_sample: Values per peak

variables_as_metadata: Variables as metadata

volcano_plot_fc_tt: Volcano plot

xvalue_interval_to_indexes: Get indexes of an interval of x-values

x_values_to_indexes: Get x-values indexes

Files in this package

specmine
specmine/NAMESPACE
specmine/data
specmine/data/propolisSampleList.rda
specmine/data/spinalCord.rda
specmine/data/cachexia.rda
specmine/data/propolis.rda
specmine/data/cassavaPPD.rda
specmine/data/datalist
specmine/R
specmine/R/preprocessing.R specmine/R/utils.R specmine/R/pca.R specmine/R/filter_dataset.R specmine/R/structure.R specmine/R/graphics.R specmine/R/regression.R specmine/R/read_spc.R specmine/R/filters_flat.R specmine/R/normalization.R specmine/R/feature_selection.R specmine/R/reading_data.R specmine/R/peaklists.R specmine/R/convert_chemospec.R specmine/R/machinelearning.R specmine/R/mzmatch_metabolite_identification.R specmine/R/ms_functions.R specmine/R/init.R specmine/R/missing_values.R specmine/R/clustering.R specmine/R/read.spc.modified.R specmine/R/stats.R specmine/R/convert_hyperspec.R specmine/R/univariate.R specmine/R/MAIT_metabolite_identification.R specmine/R/read_dx.R specmine/R/peak_alignment.R specmine/R/data_integration.R
specmine/MD5
specmine/DESCRIPTION
specmine/man
specmine/man/plot_anova.Rd specmine/man/get_value_label.Rd specmine/man/remove_metadata_variables.Rd specmine/man/fold_change.Rd specmine/man/impute_nas_mean.Rd specmine/man/kmeans_plot.Rd specmine/man/pca_pairs_kmeans_plot.Rd specmine/man/pca_screeplot.Rd specmine/man/impute_nas_value.Rd specmine/man/scaling_samples.Rd specmine/man/normalize_samples.Rd specmine/man/low_level_fusion.Rd specmine/man/get_metadata_var.Rd specmine/man/read_dataset_dx.Rd specmine/man/apply_by_sample.Rd specmine/man/scaling.Rd specmine/man/get_type.Rd specmine/man/values_per_peak.Rd specmine/man/train_models_performance.Rd specmine/man/set_x_label.Rd specmine/man/remove_variables_by_nas.Rd specmine/man/get_sample_names.Rd specmine/man/linreg_pvalue_table.Rd specmine/man/x_values_to_indexes.Rd specmine/man/remove_samples_by_nas.Rd specmine/man/plot_kstest.Rd specmine/man/set_x_values.Rd specmine/man/read_dataset_spc.Rd specmine/man/plot_ttests.Rd specmine/man/count_missing_values_per_variable.Rd specmine/man/convert_from_hyperspec.Rd specmine/man/apply_by_group.Rd specmine/man/impute_nas_knn.Rd specmine/man/first_derivative.Rd specmine/man/multifactor_aov_all_vars.Rd specmine/man/convert_from_chemospec.Rd specmine/man/read_data_csv.Rd specmine/man/background_correction.Rd specmine/man/merge_data_metadata.Rd specmine/man/pca_biplot.Rd specmine/man/missingvalues_imputation.Rd specmine/man/multifactor_aov_varexp_table.Rd specmine/man/ksTest_dataset.Rd specmine/man/plot_fold_change.Rd specmine/man/compare_regions_by_sample.Rd specmine/man/peaks_per_sample.Rd specmine/man/convert_to_hyperspec.Rd specmine/man/get_samples_names_dx.Rd specmine/man/hierarchical_clustering.Rd specmine/man/absorbance_to_transmittance.Rd specmine/man/cubic_root_transform.Rd specmine/man/pca_scoresplot3D_rgl.Rd specmine/man/get_data_as_df.Rd specmine/man/remove_data_variables.Rd specmine/man/pca_scoresplot2D.Rd specmine/man/savitzky_golay.Rd specmine/man/transmittance_to_absorbance.Rd specmine/man/tTests_dataset.Rd specmine/man/dataset_from_peaks.Rd specmine/man/kmeans_clustering.Rd specmine/man/subset_x_values_by_interval.Rd specmine/man/transform_data.Rd specmine/man/plot_spectra.Rd specmine/man/sum_dataset.Rd specmine/man/data_correction.Rd specmine/man/dendrogram_plot.Rd specmine/man/values_per_sample.Rd specmine/man/convert_to_factor.Rd specmine/man/predict_samples.Rd specmine/man/kruskalTest_dataset.Rd specmine/man/read_csvs_folder.Rd specmine/man/remove_peaks_interval_sample_list.Rd specmine/man/multiClassSummary.Rd specmine/man/correlations_test.Rd specmine/man/check_dataset.Rd specmine/man/get_data_values.Rd specmine/man/aggregate_samples.Rd specmine/man/fold_change_var.Rd specmine/man/volcano_plot_fc_tt.Rd specmine/man/clustering.Rd specmine/man/apply_by_groups.Rd specmine/man/snv_dataset.Rd specmine/man/pca_kmeans_plot3D.Rd specmine/man/set_value_label.Rd specmine/man/linreg_coef_table.Rd specmine/man/kmeans_result_df.Rd specmine/man/plot_spectra_simple.Rd specmine/man/set_metadata.Rd specmine/man/read_ms_spectra.Rd specmine/man/spinalCord.Rd specmine/man/replace_metadata_value.Rd specmine/man/count_missing_values.Rd specmine/man/remove_samples.Rd specmine/man/linreg_rsquared.Rd specmine/man/read_multiple_csvs.Rd specmine/man/propolis.Rd specmine/man/cachexia.Rd specmine/man/boxplot_vars_factor.Rd specmine/man/pca_pairs_plot.Rd specmine/man/set_sample_names.Rd specmine/man/get_metadata.Rd specmine/man/mean_centering.Rd specmine/man/count_missing_values_per_sample.Rd specmine/man/pca_robust.Rd specmine/man/get_data_value.Rd specmine/man/heatmap_correlations.Rd specmine/man/plot_kruskaltest.Rd specmine/man/get_x_label.Rd specmine/man/merge_datasets.Rd specmine/man/aov_all_vars.Rd specmine/man/read_metadata.Rd specmine/man/find_equal_samples.Rd specmine/man/offset_correction.Rd specmine/man/get_data.Rd specmine/man/read_data_spc.Rd specmine/man/multiplot.Rd specmine/man/subset_random_samples.Rd specmine/man/remove_samples_by_na_metadata.Rd specmine/man/subset_by_samples_and_xvalues.Rd specmine/man/group_peaks.Rd specmine/man/feature_selection.Rd specmine/man/multifactor_aov_pvalues_table.Rd specmine/man/recursive_feature_elimination.Rd specmine/man/linregression_onevar.Rd specmine/man/dendrogram_plot_col.Rd specmine/man/remove_peaks_interval.Rd specmine/man/shift_correction.Rd specmine/man/subset_samples_by_metadata_values.Rd specmine/man/metadata_as_variables.Rd specmine/man/peaks_per_samples.Rd specmine/man/correlation_test.Rd specmine/man/filter_feature_selection.Rd specmine/man/num_samples.Rd specmine/man/msc_correction.Rd specmine/man/correlations_dataset.Rd specmine/man/baseline_correction.Rd specmine/man/xvalue_interval_to_indexes.Rd specmine/man/subset_x_values.Rd specmine/man/log_transform.Rd specmine/man/variables_as_metadata.Rd specmine/man/is_spectra.Rd specmine/man/normalize.Rd specmine/man/train_and_predict.Rd specmine/man/pca_kmeans_plot2D.Rd specmine/man/summary_var_importance.Rd specmine/man/pca_plot_3d.Rd specmine/man/read_dataset_csv.Rd specmine/man/impute_nas_median.Rd specmine/man/stats_by_sample.Rd specmine/man/read_data_dx.Rd specmine/man/subset_metadata.Rd specmine/man/pca_importance.Rd specmine/man/get_metadata_value.Rd specmine/man/indexes_to_xvalue_interval.Rd specmine/man/smoothing_interpolation.Rd specmine/man/train_classifier.Rd specmine/man/get_peak_values.Rd specmine/man/boxplot_variables.Rd specmine/man/plot_regression_coefs_pvalues.Rd specmine/man/subset_samples.Rd specmine/man/pca_analysis_dataset.Rd specmine/man/get_x_values_as_text.Rd specmine/man/create_dataset.Rd specmine/man/remove_x_values_by_interval.Rd specmine/man/pca_biplot3D.Rd specmine/man/num_x_values.Rd specmine/man/flat_pattern_filter.Rd specmine/man/cassavaPPD.Rd specmine/man/remove_data.Rd specmine/man/plotvar_twofactor.Rd specmine/man/apply_by_variable.Rd specmine/man/impute_nas_linapprox.Rd specmine/man/replace_data_value.Rd specmine/man/get_samples_names_spc.Rd specmine/man/MAIT_identify_metabolites.Rd specmine/man/stats_by_variable.Rd specmine/man/pca_scoresplot3D.Rd specmine/man/linreg_all_vars.Rd specmine/man/propolisSampleList.Rd specmine/man/get_x_values_as_num.Rd

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