Directional Pathway-by-Pathway Interaction Maps from Genome-Scale Perturb-Seq

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Documentation for package ‘path2path’ version 0.99.4

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

as_path2path_matrix	Convert a SummarizedExperiment assay to a path2path input matrix.
as_path2path_se	Convert a path2path map to a SummarizedExperiment.
bh_populated	Benjamini-Hochberg over the populated (non-NA) cells of a matrix.
build_null_pool	Whole-pipeline permutation null calibration.
calibrate_pvalues	One-call calibrated p-values for an existing map.
dataset_tag	Dataset tag from a zscore_<tag>.csv[.gz] filename.
demo_pathways	Synthetic demonstration pathway collection
demo_z	Synthetic demonstration input matrix
jaccard_mask	Mask off-diagonal entries whose pathway pair overlaps above 'tau'.
load_pathways	Load an MSigDB collection as a named list of gene-symbol vectors.
order_by_activity	Pathway names ordered by number of significant entries (descending).
path2path	Full two-stage GSEA pipeline: z matrix -> pathway x pathway matrix.
pathway_jaccard	Pairwise Jaccard similarity of pathway gene sets (dense crossproduct).
permute_input	Whole-matrix permutation: one global row and one global column permutation.
plot_calibration	Route B diagnostics: null-pool tail versus the fitted GPD.
plot_entry	GSEA-style enrichment plot for one map entry: why is M[j, k] strong?
plot_map	Heatmap of a path2path map with significance dots.
read_input_matrix	Read a z-score CSV (rows = perturbed gene symbols in first column).
select_active	Pathways with at least 'min_sig' significant entries, as regulators and as readouts.
stage1_nes	Stage 1: per-perturbation preranked GSEA.
stage2_matrix	Stage 2: per-pathway-column GSEA in the perturbation universe.
write_result	Write pipeline outputs with dataset/collection namespacing.