Man pages for keyes-timothy/tidytof
Analyze High-dimensional Cytometry Data Using Tidy Data Principles
| as_flowFrame | Coerce an object into a 'flowFrame' |
| as_flowSet | Coerce an object into a 'flowSet' |
| as_seurat | Coerce an object into a 'SeuratObject' |
| as_SingleCellExperiment | Coerce an object into a 'SingleCellExperiment' |
| as_tof_tbl | Coerce flowFrames or flowSets into tof_tbl's. |
| as_tof_tbl.flowSet | Convert an object into a tof_tbl |
| cosine_similarity | Find the cosine similarity between two vectors |
| ddpr_data | CyTOF data from two samples: 5,000 B-cell lineage cells from... |
| ddpr_metadata | Clinical metadata for each patient sample in Good & Sarno et... |
| dot | Find the dot product between two vectors. |
| get_extension | Find the extension for a file |
| l2_normalize | L2 normalize an input vector x to a length of 1 |
| magnitude | Find the magnitude of a vector. |
| make_flowcore_annotated_data_frame | Make the AnnotatedDataFrame needed for the flowFrame class |
| metal_masterlist | A character vector of metal name patterns supported by... |
| new_tof_model | Constructor for a tof_model. |
| new_tof_tibble | Constructor for a tof_tibble. |
| phenograph_data | CyTOF data from 6,000 healthy immune cells from a single... |
| reexports | Objects exported from other packages |
| rev_asinh | Reverses arcsinh transformation with cofactor 'scale_factor'... |
| tidytof_example_data | Get paths to tidytof example data |
| tof_analyze_abundance | Perform Differential Abundance Analysis (DAA) on... |
| tof_analyze_abundance_diffcyt | Differential Abundance Analysis (DAA) with diffcyt |
| tof_analyze_abundance_glmm | Differential Abundance Analysis (DAA) with generalized linear... |
| tof_analyze_abundance_ttest | Differential Abundance Analysis (DAA) with t-tests |
| tof_analyze_expression | Perform Differential Expression Analysis (DEA) on... |
| tof_analyze_expression_diffcyt | Differential Expression Analysis (DEA) with diffcyt |
| tof_analyze_expression_lmm | Differential Expression Analysis (DEA) with linear... |
| tof_analyze_expression_ttest | Differential Expression Analysis (DEA) with t-tests |
| tof_annotate_clusters | Manually annotate tidytof-computed clusters using... |
| tof_apply_classifier | Perform developmental clustering on CyTOF data using a... |
| tof_assess_channels | Detect low-expression (i.e. potentially failed) channels in... |
| tof_assess_clusters_distance | Assess a clustering result by calculating the z-score of each... |
| tof_assess_clusters_entropy | Assess a clustering result by calculating the shannon entropy... |
| tof_assess_clusters_knn | Assess a clustering result by calculating a cell's cluster... |
| tof_assess_flow_rate | Detect flow rate abnormalities in high-dimensional cytometry... |
| tof_assess_flow_rate_tibble | Detect flow rate abnormalities in high-dimensional cytometry... |
| tof_assess_model | Assess a trained elastic net model |
| tof_assess_model_new_data | Compute a trained elastic net model's performance metrics... |
| tof_assess_model_tuning | Access a trained elastic net model's performance metrics... |
| tof_batch_correct | Perform groupwise linear rescaling of high-dimensional... |
| tof_batch_correct_quantile | Batch-correct a tibble of high-dimensional cytometry data... |
| tof_batch_correct_quantile_tibble | Batch-correct a tibble of high-dimensional cytometry data... |
| tof_batch_correct_rescale | Perform groupwise linear rescaling of high-dimensional... |
| tof_build_classifier | Calculate centroids and covariance matrices for each cell... |
| tof_calculate_flow_rate | Calculate the relative flow rates of different timepoints... |
| tof_check_model_args | Check argument specifications for a glmnet model. |
| tof_classify_cells | Classify each cell (i.e. each row) in a matrix of cancer... |
| tof_clean_metric_names | Rename glmnet's default model evaluation metrics to make them... |
| tof_cluster | Cluster high-dimensional cytometry data. |
| tof_cluster_ddpr | Perform developmental clustering on high-dimensional... |
| tof_cluster_flowsom | Perform FlowSOM clustering on high-dimensional cytometry data |
| tof_cluster_grouped | Cluster (grouped) high-dimensional cytometry data. |
| tof_cluster_kmeans | Perform k-means clustering on high-dimensional cytometry... |
| tof_cluster_phenograph | Perform PhenoGraph clustering on high-dimensional cytometry... |
| tof_cluster_tibble | Cluster (ungrouped) high-dimensional cytometry data. |
| tof_compute_km_curve | Compute a Kaplan-Meier curve from sample-level survival data |
| tof_cosine_dist | A function for finding the cosine distance between each of... |
| tof_create_grid | Create an elastic net hyperparameter search grid of a... |
| tof_create_recipe | Create a recipe for preprocessing sample-level cytometry data... |
| tof_downsample | Downsample high-dimensional cytometry data. |
| tof_downsample_constant | Downsample high-dimensional cytometry data by randomly... |
| tof_downsample_density | Downsample high-dimensional cytometry data by randomly... |
| tof_downsample_prop | Downsample high-dimensional cytometry data by randomly... |
| tof_estimate_density | Estimate the local densities for all cells in a... |
| tof_extract_central_tendency | Extract the central tendencies of CyTOF markers in each... |
| tof_extract_emd | Extract aggregated features from CyTOF data using... |
| tof_extract_features | Extract aggregated, sample-level features from CyTOF data. |
| tof_extract_jsd | Extract aggregated features from CyTOF data using the... |
| tof_extract_proportion | Extract the proportion of cells in each cluster in a... |
| tof_extract_threshold | Extract aggregated features from CyTOF data using a binary... |
| tof_find_best | Find the optimal hyperparameters for an elastic net model... |
| tof_find_cv_predictions | Calculate and store the predicted outcomes for each... |
| tof_find_emd | Find the earth-mover's distance between two numeric vectors |
| tof_find_jsd | Find the Jensen-Shannon Divergence (JSD) between two numeric... |
| tof_find_knn | Find the k-nearest neighbors of each cell in a... |
| tof_find_log_rank_threshold | Compute the log-rank test p-value for the difference between... |
| tof_find_panel_info | Use tidytof's opinionated heuristic for extracted a... |
| tof_fit_split | Fit a glmnet model and calculate performance metrics using a... |
| tof_generate_palette | Generate a color palette using tidytof. |
| tof_get_model_mixture | Get a 'tof_model”s optimal mixture (alpha) value |
| tof_get_model_outcomes | Get a 'tof_model”s outcome variable name(s) |
| tof_get_model_penalty | Get a 'tof_model”s optimal penalty (lambda) value |
| tof_get_model_training_data | Get a 'tof_model”s training data |
| tof_get_model_type | Get a 'tof_model”s model type |
| tof_get_model_x | Get a 'tof_model”s processed predictor matrix (for glmnet) |
| tof_get_model_y | Get a 'tof_model”s processed outcome variable matrix (for... |
| tof_get_panel | Get panel information from a tof_tibble |
| tof_is_numeric | Find if a vector is numeric |
| tof_knn_density | Estimate cells' local densities using K-nearest-neighbor... |
| tof_log_rank_test | Compute the log-rank test p-value for the difference between... |
| tof_make_knn_graph | Title |
| tof_make_roc_curve | Compute a receiver-operating curve (ROC) for a two-class or... |
| tof_metacluster | Metacluster clustered CyTOF data. |
| tof_metacluster_consensus | Metacluster clustered CyTOF data using consensus clustering |
| tof_metacluster_flowsom | Metacluster clustered CyTOF data using FlowSOM's built-in... |
| tof_metacluster_hierarchical | Metacluster clustered CyTOF data using hierarchical... |
| tof_metacluster_kmeans | Metacluster clustered CyTOF data using k-means clustering |
| tof_metacluster_phenograph | Metacluster clustered CyTOF data using PhenoGraph clustering |
| tof_plot_cells_density | Plot marker expression density plots |
| tof_plot_cells_embedding | Plot scatterplots of single-cell data using low-dimensional... |
| tof_plot_cells_layout | Plot force-directed layouts of single-cell data |
| tof_plot_cells_scatter | Plot scatterplots of single-cell data. |
| tof_plot_clusters_heatmap | Make a heatmap summarizing cluster marker expression patterns... |
| tof_plot_clusters_mst | Visualize clusters in CyTOF data using a minimum spanning... |
| tof_plot_clusters_volcano | Create a volcano plot from differential expression analysis... |
| tof_plot_heatmap | Make a heatmap summarizing group marker expression patterns... |
| tof_plot_model | Plot the results of a glmnet model fit on sample-level data. |
| tof_plot_model_linear | Plot the results of a linear glmnet model fit on sample-level... |
| tof_plot_model_logistic | Plot the results of a two-class glmnet model fit on... |
| tof_plot_model_multinomial | Plot the results of a multiclass glmnet model fit on... |
| tof_plot_model_survival | Plot the results of a survival glmnet model fit on... |
| tof_plot_sample_features | Make a heatmap summarizing sample marker expression patterns... |
| tof_plot_sample_heatmap | Make a heatmap summarizing sample marker expression patterns... |
| tof_postprocess | Post-process transformed CyTOF data. |
| tof_predict | Use a trained elastic net model to predict fitted values from... |
| tof_prep_recipe | Train a recipe or list of recipes for preprocessing... |
| tof_preprocess | Preprocess raw high-dimensional cytometry data. |
| tof_read_csv | Read high-dimensional cytometry data from a .csv file into a... |
| tof_read_data | Read data from an .fcs/.csv file or a directory of .fcs/.csv... |
| tof_read_fcs | Read high-dimensional cytometry data from an .fcs file into a... |
| tof_read_file | Read high-dimensional cytometry data from a single .fcs or... |
| tof_reduce_dimensions | Apply dimensionality reduction to a single-cell dataset. |
| tof_reduce_pca | Perform principal component analysis on single-cell data |
| tof_reduce_tsne | Perform t-distributed stochastic neighborhood embedding on... |
| tof_reduce_umap | Apply uniform manifold approximation and projection (UMAP) to... |
| tof_set_panel | Set panel information from a tof_tibble |
| tof_spade_density | Estimate cells' local densities as done in Spanning-tree... |
| tof_split_data | Split high-dimensional cytometry data into a training and... |
| tof_split_tidytof_reduced_dimensions | Split the dimensionality reduction data that tidytof combines... |
| tof_train_model | Train an elastic net model to predict sample-level phenomena... |
| tof_transform | Transform raw high-dimensional cytometry data. |
| tof_tune_glmnet | Tune an elastic net model's hyperparameters over multiple... |
| tof_upsample | Upsample cells into the closest cluster in a reference... |
| tof_upsample_distance | Upsample cells into the closest cluster in a reference... |
| tof_upsample_neighbor | Upsample cells into the cluster of their nearest neighbor a... |
| tof_write_csv | Write a series of .csv files from a tof_tbl |
| tof_write_data | Write high-dimensional cytometry data to a file or to a... |
| tof_write_fcs | Write a series of .fcs files from a tof_tbl |
| where | Select variables with a function |
