Man pages for wmacnair/SampleQC
Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data
| calc_pairwise_mmds | calc_pairwise_mmds |
| dot-add_annot_vars | Adds user-specified annotation variables |
| dot-add_log_counts | Add log counts to qc_dt |
| dot-add_log_feats | Add log feats to qc_dt |
| dot-add_logit_mito | Add logit-transformed mitochondrial proportions to qc_dt |
| dot-add_qc_annots | Adds sample-level annotations for each known QC metric |
| dot-add_splice_ratio | Add log splice ratio to qc_dt |
| dot-add_unknown_metrics | Adds metrics that SampleQC doesn't have specific functions... |
| dot-assemble_fit_results | Puts results from fitting models into SingleCellExperiment... |
| dot-calc_ellipses_dt | Calculates path for an ellipse based on 2D mu and sigma... |
| dot-calc_mat_list | Splits qc_dt into list of matrices, one for each sample |
| dot-calc_mmd_mat | Calculates mean MMD distances between all pairs of samples |
| dot-calc_one_ellipse | Calculates path for an ellipse based on 2D mu and sigma... |
| dot-calc_outliers_dt | Calculate outliers for each cell |
| dot-calc_p_jk_proportions | DEPRECATED: Calculate proportions of cells within each sample... |
| dot-check_fit_params | Checks that the parameters specified are ok |
| dot-check_is_qc_obj | Checks whether a given sce object is a SampleQC object |
| dot-check_qc_dt | Checks that output is ok |
| dot-cluster_mmd_graph | Cluster igraph object using Louvain clustering |
| dot-dist_fn | Wrapper for cpp MMD distance function |
| dot-draw_alpha_j | Draws random parameters for sample shifts |
| dot-draw_beta_k | Draws random parameters for mixture model components |
| dot-draw_delta_jk | Draws random parameters for mixture model components |
| dot-draw_dir_0 | Determines Dirichlet parameter for p_jk draws |
| dot-draw_expt_params | Draws experiment-level parameters |
| dot-draw_mu_0s | Draws centre of sample group |
| dot-draw_out_j | Draws random parameters to determine how to do outliers |
| dot-draw_outliers | Which cells are outliers? |
| dot-draw_p_jk | Draws random parameters for mixing parameters |
| dot-draw_p_loss_0s | Draws group-level probabilities of reads being lost in... |
| dot-draw_p_out_0s | Sample group-level probabilities of cells being outliers |
| dot-draw_samples | Randomly splits up N cells into J samples with different... |
| dot-draw_sel_ks | Determines which components are observed in each sample group |
| dot-draw_Sigma_k | Draws random parameters for mixture model covariances |
| dot-draw_theta_0s | Draws group-level probabilities of cells being outliers |
| dot-draw_z | Draws latent true component for each cell |
| dot-embed_mds | MDS embedding of MMD distances |
| dot-embed_umap | Calculates non-linear embeddings of MMD distances calculated... |
| dot-fit_one_sampleqc | Fits 'SampleQC' model to one cluster of samples |
| dot-init_clusts | Initializes clusters |
| dot-init_qc_dt | Initializes qc_dt object |
| dot-make_mmd_graph | Build igraph object from MMD matrix |
| dot-make_toy_qc_df | Generate fake qc_df object for testing |
| dot-make_toy_sce | Generate fake sce object for testing |
| dot-plot_one_embedding | Plots non-linear embeddings of MMD distances calculated by... |
| dot-process_annot_vars | Checks annotation variables |
| dot-process_outputs | Gathers results simulated for individual sample groups... |
| dot-sim_ok_cells | Simulates healthy cells |
| dot-sim_outliers | Simulates outliers from ok cells |
| dot-sim_sample_group | Simulates QC metrics for one group of samples |
| fit_sampleqc | Fits 'SampleQC' model to one cluster of samples |
| fit_sampleqc_mle_cpp | Fits a multivariate Gaussian mixture model to given data via... |
| fit_sampleqc_robust_cpp | Robustly fits a multivariate Gaussian mixture model to given... |
| get_n_groups | Extracts number of groups |
| get_outliers | get_outliers |
| list_known_metrics | Shows the list of QC metrics that for which 'SampleQC'... |
| make_qc_dt | Checks specified QC metrics and makes data.table for input to... |
| make_sampleqc_report | make_sampleqc_report |
| mmd_fn | Calculate MMD between two matrices “A Kernel Two-Sample... |
| plot_alpha_js | plot_alpha_js |
| plot_alpha_js_likelihoods | plot_alpha_js_likelihoods |
| plot_beta_ks | plot_beta_ks |
| plot_embeddings | plot_embeddings |
| plot_fit_over_biaxials | plot_fit_over_biaxials |
| plot_mmd_heatmap | plot_mmd_heatmap |
| plot_outliers | plot_outliers |
| SampleQC | SampleQC: robust multivariate, multi-celltype, multi-sample... |
| simulate_qcs | simulate_qcs |
| subsample_mmd_fn | Calculate mean subsampled MMD between two matrices |
