Man pages for keyes-timothy/tidytof
Analyze High-dimensional Cytometry Data Using Tidy Data Principles

as_flowFrameCoerce an object into a 'flowFrame'
as_flowSetCoerce an object into a 'flowSet'
as_seuratCoerce an object into a 'SeuratObject'
as_SingleCellExperimentCoerce an object into a 'SingleCellExperiment'
as_tof_tblCoerce flowFrames or flowSets into tof_tbl's.
as_tof_tbl.flowSetConvert an object into a tof_tbl
cosine_similarityFind the cosine similarity between two vectors
ddpr_dataCyTOF data from two samples: 5,000 B-cell lineage cells from...
ddpr_metadataClinical metadata for each patient sample in Good & Sarno et...
dotFind the dot product between two vectors.
get_extensionFind the extension for a file
l2_normalizeL2 normalize an input vector x to a length of 1
magnitudeFind the magnitude of a vector.
make_flowcore_annotated_data_frameMake the AnnotatedDataFrame needed for the flowFrame class
metal_masterlistA character vector of metal name patterns supported by...
new_tof_modelConstructor for a tof_model.
new_tof_tibbleConstructor for a tof_tibble.
phenograph_dataCyTOF data from 6,000 healthy immune cells from a single...
reexportsObjects exported from other packages
rev_asinhReverses arcsinh transformation with cofactor 'scale_factor'...
tidytof_example_dataGet paths to tidytof example data
tof_analyze_abundancePerform Differential Abundance Analysis (DAA) on...
tof_analyze_abundance_diffcytDifferential Abundance Analysis (DAA) with diffcyt
tof_analyze_abundance_glmmDifferential Abundance Analysis (DAA) with generalized linear...
tof_analyze_abundance_ttestDifferential Abundance Analysis (DAA) with t-tests
tof_analyze_expressionPerform Differential Expression Analysis (DEA) on...
tof_analyze_expression_diffcytDifferential Expression Analysis (DEA) with diffcyt
tof_analyze_expression_lmmDifferential Expression Analysis (DEA) with linear...
tof_analyze_expression_ttestDifferential Expression Analysis (DEA) with t-tests
tof_annotate_clustersManually annotate tidytof-computed clusters using...
tof_apply_classifierPerform developmental clustering on CyTOF data using a...
tof_assess_channelsDetect low-expression (i.e. potentially failed) channels in...
tof_assess_clusters_distanceAssess a clustering result by calculating the z-score of each...
tof_assess_clusters_entropyAssess a clustering result by calculating the shannon entropy...
tof_assess_clusters_knnAssess a clustering result by calculating a cell's cluster...
tof_assess_flow_rateDetect flow rate abnormalities in high-dimensional cytometry...
tof_assess_flow_rate_tibbleDetect flow rate abnormalities in high-dimensional cytometry...
tof_assess_modelAssess a trained elastic net model
tof_assess_model_new_dataCompute a trained elastic net model's performance metrics...
tof_assess_model_tuningAccess a trained elastic net model's performance metrics...
tof_batch_correctPerform groupwise linear rescaling of high-dimensional...
tof_batch_correct_quantileBatch-correct a tibble of high-dimensional cytometry data...
tof_batch_correct_quantile_tibbleBatch-correct a tibble of high-dimensional cytometry data...
tof_batch_correct_rescalePerform groupwise linear rescaling of high-dimensional...
tof_build_classifierCalculate centroids and covariance matrices for each cell...
tof_calculate_flow_rateCalculate the relative flow rates of different timepoints...
tof_check_model_argsCheck argument specifications for a glmnet model.
tof_classify_cellsClassify each cell (i.e. each row) in a matrix of cancer...
tof_clean_metric_namesRename glmnet's default model evaluation metrics to make them...
tof_clusterCluster high-dimensional cytometry data.
tof_cluster_ddprPerform developmental clustering on high-dimensional...
tof_cluster_flowsomPerform FlowSOM clustering on high-dimensional cytometry data
tof_cluster_groupedCluster (grouped) high-dimensional cytometry data.
tof_cluster_kmeansPerform k-means clustering on high-dimensional cytometry...
tof_cluster_phenographPerform PhenoGraph clustering on high-dimensional cytometry...
tof_cluster_tibbleCluster (ungrouped) high-dimensional cytometry data.
tof_compute_km_curveCompute a Kaplan-Meier curve from sample-level survival data
tof_cosine_distA function for finding the cosine distance between each of...
tof_create_gridCreate an elastic net hyperparameter search grid of a...
tof_create_recipeCreate a recipe for preprocessing sample-level cytometry data...
tof_downsampleDownsample high-dimensional cytometry data.
tof_downsample_constantDownsample high-dimensional cytometry data by randomly...
tof_downsample_densityDownsample high-dimensional cytometry data by randomly...
tof_downsample_propDownsample high-dimensional cytometry data by randomly...
tof_estimate_densityEstimate the local densities for all cells in a...
tof_extract_central_tendencyExtract the central tendencies of CyTOF markers in each...
tof_extract_emdExtract aggregated features from CyTOF data using...
tof_extract_featuresExtract aggregated, sample-level features from CyTOF data.
tof_extract_jsdExtract aggregated features from CyTOF data using the...
tof_extract_proportionExtract the proportion of cells in each cluster in a...
tof_extract_thresholdExtract aggregated features from CyTOF data using a binary...
tof_find_bestFind the optimal hyperparameters for an elastic net model...
tof_find_cv_predictionsCalculate and store the predicted outcomes for each...
tof_find_emdFind the earth-mover's distance between two numeric vectors
tof_find_jsdFind the Jensen-Shannon Divergence (JSD) between two numeric...
tof_find_knnFind the k-nearest neighbors of each cell in a...
tof_find_log_rank_thresholdCompute the log-rank test p-value for the difference between...
tof_find_panel_infoUse tidytof's opinionated heuristic for extracted a...
tof_fit_splitFit a glmnet model and calculate performance metrics using a...
tof_generate_paletteGenerate a color palette using tidytof.
tof_get_model_mixtureGet a 'tof_model”s optimal mixture (alpha) value
tof_get_model_outcomesGet a 'tof_model”s outcome variable name(s)
tof_get_model_penaltyGet a 'tof_model”s optimal penalty (lambda) value
tof_get_model_training_dataGet a 'tof_model”s training data
tof_get_model_typeGet a 'tof_model”s model type
tof_get_model_xGet a 'tof_model”s processed predictor matrix (for glmnet)
tof_get_model_yGet a 'tof_model”s processed outcome variable matrix (for...
tof_get_panelGet panel information from a tof_tibble
tof_is_numericFind if a vector is numeric
tof_knn_densityEstimate cells' local densities using K-nearest-neighbor...
tof_log_rank_testCompute the log-rank test p-value for the difference between...
tof_make_knn_graphTitle
tof_make_roc_curveCompute a receiver-operating curve (ROC) for a two-class or...
tof_metaclusterMetacluster clustered CyTOF data.
tof_metacluster_consensusMetacluster clustered CyTOF data using consensus clustering
tof_metacluster_flowsomMetacluster clustered CyTOF data using FlowSOM's built-in...
tof_metacluster_hierarchicalMetacluster clustered CyTOF data using hierarchical...
tof_metacluster_kmeansMetacluster clustered CyTOF data using k-means clustering
tof_metacluster_phenographMetacluster clustered CyTOF data using PhenoGraph clustering
tof_plot_cells_densityPlot marker expression density plots
tof_plot_cells_embeddingPlot scatterplots of single-cell data using low-dimensional...
tof_plot_cells_layoutPlot force-directed layouts of single-cell data
tof_plot_cells_scatterPlot scatterplots of single-cell data.
tof_plot_clusters_heatmapMake a heatmap summarizing cluster marker expression patterns...
tof_plot_clusters_mstVisualize clusters in CyTOF data using a minimum spanning...
tof_plot_clusters_volcanoCreate a volcano plot from differential expression analysis...
tof_plot_heatmapMake a heatmap summarizing group marker expression patterns...
tof_plot_modelPlot the results of a glmnet model fit on sample-level data.
tof_plot_model_linearPlot the results of a linear glmnet model fit on sample-level...
tof_plot_model_logisticPlot the results of a two-class glmnet model fit on...
tof_plot_model_multinomialPlot the results of a multiclass glmnet model fit on...
tof_plot_model_survivalPlot the results of a survival glmnet model fit on...
tof_plot_sample_featuresMake a heatmap summarizing sample marker expression patterns...
tof_plot_sample_heatmapMake a heatmap summarizing sample marker expression patterns...
tof_postprocessPost-process transformed CyTOF data.
tof_predictUse a trained elastic net model to predict fitted values from...
tof_prep_recipeTrain a recipe or list of recipes for preprocessing...
tof_preprocessPreprocess raw high-dimensional cytometry data.
tof_read_csvRead high-dimensional cytometry data from a .csv file into a...
tof_read_dataRead data from an .fcs/.csv file or a directory of .fcs/.csv...
tof_read_fcsRead high-dimensional cytometry data from an .fcs file into a...
tof_read_fileRead high-dimensional cytometry data from a single .fcs or...
tof_reduce_dimensionsApply dimensionality reduction to a single-cell dataset.
tof_reduce_pcaPerform principal component analysis on single-cell data
tof_reduce_tsnePerform t-distributed stochastic neighborhood embedding on...
tof_reduce_umapApply uniform manifold approximation and projection (UMAP) to...
tof_set_panelSet panel information from a tof_tibble
tof_spade_densityEstimate cells' local densities as done in Spanning-tree...
tof_split_dataSplit high-dimensional cytometry data into a training and...
tof_split_tidytof_reduced_dimensionsSplit the dimensionality reduction data that tidytof combines...
tof_train_modelTrain an elastic net model to predict sample-level phenomena...
tof_transformTransform raw high-dimensional cytometry data.
tof_tune_glmnetTune an elastic net model's hyperparameters over multiple...
tof_upsampleUpsample cells into the closest cluster in a reference...
tof_upsample_distanceUpsample cells into the closest cluster in a reference...
tof_upsample_neighborUpsample cells into the cluster of their nearest neighbor a...
tof_write_csvWrite a series of .csv files from a tof_tbl
tof_write_dataWrite high-dimensional cytometry data to a file or to a...
tof_write_fcsWrite a series of .fcs files from a tof_tbl
whereSelect variables with a function
keyes-timothy/tidytof documentation built on Aug. 28, 2024, 8:37 a.m.