Package index • dmsa

The two-call interface

Declare the design once, run it once.

dmsa_frame(): Declare a DMSA analysis frame
dmsa_report(): Run a declared frame and deliver figures, tables and a summary
dmsa_report_panels(): Build the whole report: panel 1 once, panels 2 and 3 per firing system

Working from a SummarizedExperiment.

The directional chain and the three lenses.

dmsa_align(): Build the aligned sign s_j for a set of probes
dmsa_directions(): The direction calls DMSA ships with
dmsa_triangulate(): Three complementary lenses on the same family
dmsa_test(): Fixed-sign or expected-sign DMSA pooled test
dmsa_pdance(): The p-dance test: does a finding's p-value survive a change of analysis set?
dmsa_score(): Subject-level aligned tone score
dmsa_scores(): Aligned set scores, and the alternatives worth comparing against
dmsa_relweights(): Outcome-free reliability weights for aligned probes
dmsa_perm_pvalue(): Permutation p-value for a DMSA statistic
dmsa_omnibus(): Directionless omnibus test of a categorical focal exposure over a set

dmsa_sets(): Load a selection cascade (system > module > gene > probe)
dmsa_select(): Select a set of units from a cascade
dmsa_cascade(): Gated hierarchical DMSA with level-specific inference
dmsa_systems(): The systems available in a cascade, with the short names to select them by
dmsa_levels(): Gated hierarchical DMSA on the pooled aligned statistic
dmsa_tree(): Build a cascade tree for a set of probes from a reference bundle
dmsa_sets_check(): Validate a candidate cascade before using it
dmsa_sets_template(): Write a cascade template and the instructions for building one
dmsa_cascade_null(): Null statistics for cascade calibration

dmsa_polarity(): Load a gene-to-system polarity table
dmsa_polarity_check(): Validate a candidate polarity table
dmsa_polarity_for(): Polarity table for one system, in the form dmsa_align() wants
dmsa_polarity_fetch(): Draft polarity signs for a panel from public databases
dmsa_polarity_review(): Rows of a polarity table that need a human decision
dmsa_polarity_sources(): Which public resources DMSA can draft polarity from, and what each is good for
dmsa_reference(): Construct a DMSA reference bundle
dmsa_reference_csv(): Read a user-supplied system / module / gene csv as a reference bundle
dmsa_reference_read(): Read a reference bundle from CSV files
dmsa_reference_template(): Write a template csv for a user-supplied reference
dmsa_reference_write(): Write a reference bundle to a directory
dmsa_evidence(): Module-level evidence and citations for a cascade, selection or frame
alpha_polarity(): Alpha panel gene -> system-activation polarity (bundled, DRAFT)
alpha_gene_systems(): Alpha panel gene -> system map (bundled)
alpha_reference(): The bundled Project Alpha tables as a reference bundle
alpha_design(): Project Alpha build contracts

dmsa_design(): Declare a DMSA design: covariates, dependence, and permutation blocks
dmsa_check_design(): Validate a design against the data before fitting
dmsa_model(): One model, block-permutation calibrated, for any term
dmsa_model_omnibus(): Omnibus across the score projections
dmsa_fit(): Fit, pool and permute a DMSA set test under a declared design
dmsa_moderate(): Moderated DMSA (mDMSA)
dmsa_change(): Two-wave change-score DMSA: time x methylation x factor
dmsa_outcome(): Test an aligned tone score against a non-Gaussian outcome
dmsa_contrasts(): Expand a categorical focal exposure into one directional design per contrast
dmsa_contrast_adjust(): Correct p-values across the contrasts of one categorical exposure
dmsa_mvalues(): M-value transform with clamping
dmsa_gate(): Gated hierarchical DMSA: one score, one model, level-local correction
dmsa_balance(): Per-system coverage and polarity balance

dmsa_plot_genes(): Panel 2: gene level inside one system
dmsa_plot_locus(): Locus figure: chromosome, gene with CpG lollipops, and per-CpG effects
dmsa_plot_locus_gviz(): The locus panel drawn by Gviz
dmsa_plot_probes(): Panel 3: probe level, with the CpG-to-expression direction applied
dmsa_plot_systems(): Panel 1: dense arm against sparse arm, every system
dmsa_gene_model(): A gene's exon, intron and UTR structure on real coordinates
dmsa_gene_model_check(): Check a gene model before drawing from it

dmsa_probe_coords(): Probe genomic coordinates, without Bioconductor
dmsa_probe_annotation_template(): Write a template script that fetches probe coordinates from Bioconductor
dmsa_write_coords(): Save a coordinate table so the lookup never has to be repeated
dmsa_test_drive(): Re-run the frame's test drive