Metrics for Similarity Matrices


[Up] [Top]

Documentation for package ‘matric’ version 0.2.0

Help Pages

bin Bin values into increasingly wider bins
cellhealth Cell Painting dataset of CRISPR perturbations.
cellhealthmetrics Quality metrics for Cell Painting dataset of CRISPR perturbations.
cosine_sparse Compute similarity between pairs of rows of a matrix
drop_annotation Drop row annotations.
get_annotation Get row annotations.
get_p_value Compute p-value against null distribution
matric matric: Metrics for Similarity Matrices
null_distribution Compute null distribution for a set of metrics
null_distribution_helper Compute null distribution of metrics
pearson_sparse Compute similarity between pairs of rows of a matrix
preprocess_data Preprocess data. 'preprocess_data' preprocesses data.
sim_annotate Annotate a melted similarity matrix.
sim_calculate Calculate a melted similarity matrix.
sim_calculate_ij Calculate similarities given pairs of rows
sim_collate Collate several subsets of a melted similarity matrix, required for computing metrics.
sim_filter_all_same Filter a melted similarity matrix to keep pairs with the same values in specific columns.
sim_filter_all_same_keep_some Filter a melted similarity matrix to keep pairs with the same values in specific columns, and keep only some of these pairs.
sim_filter_keep_or_drop_some Filter a melted similarity matrix to remove or keep specified rows.
sim_filter_some_different_drop_some Filter a melted similarity matrix to keep pairs with the same values in specific columns, and other constraints.
sim_metrics Compute metrics.
sim_metrics_helper Helper function to compute metrics.
sim_metrics_signif Report p-values for metrics
sim_new Constructor for 'matric_sim' S3 class.
sim_plot Plot a melted similarity matrix.
sim_read Read similarity matrix.
sim_restore Restorer for 'matric_sim' S3 class.
sim_validate Validator for 'matric_sim' S3 class.
sim_wider Widen a symmetric melted similarity matrix.
sim_write Write similarity matrix.
sparse_pairwise Compute similarity between pairs of rows of a matrix
sparse_similarity Compute similarity between pairs of rows of a matrix
tcrossprod_ij Compute cross product between two sets of rows of a matrix.