Man pages for antonvsdata/amp
Smoothing Metabolomics Analyses

align_batchesAlign features between batches
assign_cluster_idAssign Cluster ID to features
autoplot.lmerModAutoplot 'lme4::lmerMod'
cluster_featuresCluster correlated features
cohens_dCohen's D
combined_dataRetrieve both sample information and features
compress_clustersCompress clusters of features to a single feature
construct_MetaboSetConstruct MetaboSet objects
correct_driftCorrect drift using cubic spline
dc_cubic_splineFit a cubic spline to correct drift
dobcBatch correction
drop_flaggedDrop flagged features
drop_qcsDrop QC samples
exponentialExponential function
find_clustersExtract the densely connected clusters
find_connectionsFind out which features are correlated within a specified...
finish_logFinish a log
finite_helpersSummary statistics of finite elements
fit_rfFit Random Forest
flagExtract flags of features
flag_detectionFlag features with low detection rate
flag_qualityFlag low-quality features
flag_reportA report of flagged features
flattenFlatten dataframe contains matrix
fold_changeFold change
geom_factoryFactory function to control 'ggplot2::geom_xxx' functions
get.layoutCalcurate layout matrix for 'ggmultiplot'
importance_rfFeature importance in random forest
impute_rfImpute missing values using random forest
impute_simpleSimple imputation
init_logInitialize log to a file
inspect_dcFlag the results of drift correction
inverse_normalizeInverse-rank normalization
join_fDataJoin new columns to feature data
join_resultsJoin results to a MetaboSet object
log_stateGet the current logging state
log_textLog text to the current log file
manhattan_plotManhattan plot
mark_nasMark specified values as missing
mark_qcsReplace NA values in pheno data columns with "QC"
merge_batchesMerge MetaboSet objects of batches together
merge_exprsPartially replace exprs field with new values
merge_metabosetsMerge MetaboSet objects together
MetaboSet-classAn S4 class used to represent LC-MS datasets
normalize_batchesNormalize batches
pca_bhattacharyya_distBhattacharyya distance between bathces in PCA space
perform_aucArea under curve
perform_correlation_testsPerform correlation tests
perform_homoscedasticity_testsTest homoscedasticity
perform_kruskal_wallisPerform Kruskal-Wallis Rank Sum Tests
perform_lmLinear models
perform_lmerLinear mixed models
perform_logisticLogistic regression
perform_oneway_anovaPerform ANOVA
perform_pairwise_t_testPerform pairwise t-tests
perform_repeatabilityCompute repeatability measures
perform_t_testPerform t-tests
plot_dendrogramDraw dendrograms
plot_dist_densityDistance density plot
plot_effect_heatmapDraw a heatmap of effects between variables, such as...
plot_injection_lmEstimate the magnitude of drift
plot_labelAttach label to 'ggplot2::ggplot'
plot_pcaPCA scatter plot
plot_pca_arrowsPCA plot with arrows
plot_pca_hexbinPCA hexbin plot
plot_pca_loadingsPCA loadings plot
plot_p_histogramHistogram of p-values
plot_qualityPlot quality metrics
plot_sample_boxplotsPlot a boxplot for each sample
plot_sample_heatmapDraw heatmaps
plot_tsnet-SNE scatter plot
plot_tsne_arrowst-SNE plot with arrows
plot_tsne_hexbint-SNE hexbin plot
prop_foundProportion of non-missing values in a vector
prop_naProportion of NA values in a vector
pull_clustersExtract information of the features in clusters
read_from_excelRead formatted Excel files
ruvs_qcRemove Unwanted Variation
save_batch_plotsSave batch correction plots
save_dc_plotsDrift correction plots
save_group_boxplotsSave box plots of each feature by group
save_group_lineplotsSave line plots with errorbars by group
save_lm_diagnostic_plotsPlot model diagnostics
save_plotSave plot to PDF
save_subject_line_plotsSave line plots with mean
scale-MetaboSet-methodScale exprs data
summary_statisticsSummary statistics
visualizationsWrite all relevant visualizations to pdf
visualize_clustersVisualize clusters of features
volcano_plotVolcano plot
write_to_excelWrite results to Excel file
antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.