Man pages for wmacnair/SampleQC
Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data

calc_pairwise_mmdscalc_pairwise_mmds
dot-add_annot_varsAdds user-specified annotation variables
dot-add_log_countsAdd log counts to qc_dt
dot-add_log_featsAdd log feats to qc_dt
dot-add_logit_mitoAdd logit-transformed mitochondrial proportions to qc_dt
dot-add_qc_annotsAdds sample-level annotations for each known QC metric
dot-add_splice_ratioAdd log splice ratio to qc_dt
dot-add_unknown_metricsAdds metrics that SampleQC doesn't have specific functions...
dot-assemble_fit_resultsPuts results from fitting models into SingleCellExperiment...
dot-calc_ellipses_dtCalculates path for an ellipse based on 2D mu and sigma...
dot-calc_mat_listSplits qc_dt into list of matrices, one for each sample
dot-calc_mmd_matCalculates mean MMD distances between all pairs of samples
dot-calc_one_ellipseCalculates path for an ellipse based on 2D mu and sigma...
dot-calc_outliers_dtCalculate outliers for each cell
dot-calc_p_jk_proportionsDEPRECATED: Calculate proportions of cells within each sample...
dot-check_fit_paramsChecks that the parameters specified are ok
dot-check_is_qc_objChecks whether a given sce object is a SampleQC object
dot-check_qc_dtChecks that output is ok
dot-cluster_mmd_graphCluster igraph object using Louvain clustering
dot-dist_fnWrapper for cpp MMD distance function
dot-draw_alpha_jDraws random parameters for sample shifts
dot-draw_beta_kDraws random parameters for mixture model components
dot-draw_delta_jkDraws random parameters for mixture model components
dot-draw_dir_0Determines Dirichlet parameter for p_jk draws
dot-draw_expt_paramsDraws experiment-level parameters
dot-draw_mu_0sDraws centre of sample group
dot-draw_out_jDraws random parameters to determine how to do outliers
dot-draw_outliersWhich cells are outliers?
dot-draw_p_jkDraws random parameters for mixing parameters
dot-draw_p_loss_0sDraws group-level probabilities of reads being lost in...
dot-draw_p_out_0sSample group-level probabilities of cells being outliers
dot-draw_samplesRandomly splits up N cells into J samples with different...
dot-draw_sel_ksDetermines which components are observed in each sample group
dot-draw_Sigma_kDraws random parameters for mixture model covariances
dot-draw_theta_0sDraws group-level probabilities of cells being outliers
dot-draw_zDraws latent true component for each cell
dot-embed_mdsMDS embedding of MMD distances
dot-embed_umapCalculates non-linear embeddings of MMD distances calculated...
dot-fit_one_sampleqcFits 'SampleQC' model to one cluster of samples
dot-init_clustsInitializes clusters
dot-init_qc_dtInitializes qc_dt object
dot-make_mmd_graphBuild igraph object from MMD matrix
dot-make_toy_qc_dfGenerate fake qc_df object for testing
dot-make_toy_sceGenerate fake sce object for testing
dot-plot_one_embeddingPlots non-linear embeddings of MMD distances calculated by...
dot-process_annot_varsChecks annotation variables
dot-process_outputsGathers results simulated for individual sample groups...
dot-sim_ok_cellsSimulates healthy cells
dot-sim_outliersSimulates outliers from ok cells
dot-sim_sample_groupSimulates QC metrics for one group of samples
fit_sampleqcFits 'SampleQC' model to one cluster of samples
fit_sampleqc_mle_cppFits a multivariate Gaussian mixture model to given data via...
fit_sampleqc_robust_cppRobustly fits a multivariate Gaussian mixture model to given...
get_n_groupsExtracts number of groups
get_outliersget_outliers
list_known_metricsShows the list of QC metrics that for which 'SampleQC'...
make_qc_dtChecks specified QC metrics and makes data.table for input to...
make_sampleqc_reportmake_sampleqc_report
mmd_fnCalculate MMD between two matrices “A Kernel Two-Sample...
plot_alpha_jsplot_alpha_js
plot_alpha_js_likelihoodsplot_alpha_js_likelihoods
plot_beta_ksplot_beta_ks
plot_embeddingsplot_embeddings
plot_fit_over_biaxialsplot_fit_over_biaxials
plot_mmd_heatmapplot_mmd_heatmap
plot_outliersplot_outliers
SampleQCSampleQC: robust multivariate, multi-celltype, multi-sample...
simulate_qcssimulate_qcs
subsample_mmd_fnCalculate mean subsampled MMD between two matrices
wmacnair/SampleQC documentation built on Nov. 18, 2022, 5 p.m.