specmine: Metabolomics and Spectral Data Analysis and Mining

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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 .

Author
Christopher Costa <chrisbcl@hotmail.com>, Marcelo Maraschin <mtocsy@gmail.com>, Miguel Rocha <mrocha@di.uminho.pt>
Date of publication
2015-11-10 11:08:16
Maintainer
Christopher Costa <chrisbcl@hotmail.com>
License
GPL (>= 2)
Version
1.0

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
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_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
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