Package: dmsa 0.99.11

Tsachi Ein-Dor

dmsa: Directional Methylation Set Analysis

Aligns probe-level methylation effects to their predicted effect on gene expression and, for system-level analysis, to each gene's curated polarity with respect to the system's activation tone (e.g. NR3C1 opposes HPA-axis activation). Pools the aligned coefficients with fixed-sign or expected-sign estimators and reports coverage and activation/brake balance per set. Ships the Project Alpha gene-system map, a gene-to-system polarity table carrying a stated source and review flag on every row, and a curated system > module > gene > probe selection cascade whose module labels carry literature-audited evidence tiers and citations; genes without a polarity entry must be specified by the user.

Authors:Tsachi Ein-Dor [aut, cre, fnd]

dmsa_0.99.11.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dmsa/json (API)

# Install 'dmsa' in R:
install.packages('dmsa', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/teindor/dmsa/issues

Pkgdown/docs site:https://teindor.github.io

On CRAN:

Conda:

dnamethylationdifferentialmethylationmethylationarraygenesetenrichmentgeneexpressionepigeneticsmicroarraycoveragestatisticalmethodmultiplecomparisonregressionsoftware

3.48 score 71 exports 18 dependencies

Last updated from:958def1e80. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING231
linux-develOK626
source / vignettesOK198
linux-releaseOK448
macos-releaseOK482
macos-oldrelOK532
windows-develOK641
windows-releaseOK646
windows-oldrelOK483
wasm-releaseOK155

Exports:alpha_designalpha_gene_systemsalpha_polarityalpha_referencealpha_reference_checkdmsa_aligndmsa_balancedmsa_bfdr_selectdmsa_cascadedmsa_cascade_nulldmsa_changedmsa_check_designdmsa_contrast_adjustdmsa_contrastsdmsa_coveragedmsa_cpg_columnsdmsa_designdmsa_directionsdmsa_evidencedmsa_fitdmsa_framedmsa_gatedmsa_gene_modeldmsa_gene_model_checkdmsa_importdmsa_levelsdmsa_lfdrdmsa_mediatedmsa_modeldmsa_model_omnibusdmsa_moderatedmsa_mvaluesdmsa_omnibusdmsa_outcomedmsa_pdancedmsa_perm_pvaluedmsa_plot_genesdmsa_plot_locusdmsa_plot_locus_gvizdmsa_plot_probesdmsa_plot_systemsdmsa_polaritydmsa_polarity_checkdmsa_polarity_fetchdmsa_polarity_fordmsa_polarity_reviewdmsa_polarity_sourcesdmsa_probe_annotation_templatedmsa_probe_coordsdmsa_referencedmsa_reference_csvdmsa_reference_readdmsa_reference_templatedmsa_reference_writedmsa_relweightsdmsa_reportdmsa_report_panelsdmsa_save_analysis_setdmsa_scoredmsa_scoresdmsa_sedmsa_selectdmsa_setsdmsa_sets_checkdmsa_sets_templatedmsa_systemsdmsa_testdmsa_test_drivedmsa_treedmsa_triangulatedmsa_write_coords

Dependencies:abindBiobaseBiocGenericsdata.tableDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

One door in: from any preprocessing pipeline to DMSA
The adapter in one example | The recipes | Does the pipeline choice change the answer? A real-data check | Session info
Rendered frompipelines.Rmdusingknitr::rmarkdown

Last update: 2026-08-22
Started: 2026-08-22

Reading direction from methylation: a first DMSA analysis
The problem this package exists to solve | What a direction-blind test sees | The alignment step | Running the three lenses | Which lens fires is itself a result | What DMSA does not do | Moving to real data
Rendered fromdmsa.Rmdusingknitr::rmarkdown

Last update: 2026-08-21
Started: 2026-08-21

Readme and manuals

Help Manual

Help pageTopics
Project Alpha build contractsalpha_design
Alpha panel gene -> system map (bundled)alpha_gene_systems
Alpha panel gene -> system-activation polarity (bundled)alpha_polarity
The bundled Project Alpha biological referencealpha_reference
Integrity of the bundled Alpha biological referencealpha_reference_check
Build the aligned sign s_j for a set of probesdmsa_align
Per-system coverage and polarity balancedmsa_balance
Select units by Bayesian FDRdmsa_bfdr_select
Gated hierarchical DMSA with level-specific inferencedmsa_cascade
Null statistics for cascade calibrationdmsa_cascade_null
Two-wave change-score DMSA: time x methylation x factordmsa_change
Validate a design against the data before fittingdmsa_check_design
Correct p-values across the contrasts of one categorical exposuredmsa_contrast_adjust
Expand a categorical focal exposure into one directional design per contrastdmsa_contrasts
Coverage report: the reference vs the testable datadmsa_coverage
Select CpG measurement columns by name patterndmsa_cpg_columns
Declare a DMSA design: covariates, dependence, and permutation blocksdmsa_design
The direction calls DMSA ships withdmsa_directions
Module-level evidence and citations for a cascade, selection or framedmsa_evidence
Fit, pool and permute a DMSA set test under a declared designdmsa_fit
Declare a DMSA analysis framedmsa_frame
Gated hierarchical DMSA: one score, one model, level-local correctiondmsa_gate
A gene's exon, intron and UTR structure on real coordinatesdmsa_gene_model
Check a gene model before drawing from itdmsa_gene_model_check
Import a preprocessing pipeline's result for DMSAdmsa_import dmsa_import.character dmsa_import.data.frame dmsa_import.default dmsa_import.list dmsa_import.matrix
Gated hierarchical DMSA on the pooled aligned statisticdmsa_levels
Local false discovery rate by central matchingdmsa_lfdr
Latent moderated mediation over DMSA system tonesdmsa_mediate
One model, block-permutation calibrated, for any termdmsa_model
Omnibus across the score projectionsdmsa_model_omnibus
Moderated DMSA (mDMSA)dmsa_moderate
M-value transform with clampingdmsa_mvalues
Directionless omnibus test of a categorical focal exposure over a setdmsa_omnibus
Test an aligned tone score against a non-Gaussian outcomedmsa_outcome
The p-dance test: does a finding's p-value survive a change of analysis set?dmsa_pdance
Permutation p-value for a DMSA statisticdmsa_perm_pvalue
Panel 2: gene level inside one systemdmsa_plot_genes
Locus figure: chromosome, gene with CpG lollipops, and per-CpG effectsdmsa_plot_locus
The locus panel drawn by Gvizdmsa_plot_locus_gviz
Panel 3: probe level, with the CpG-to-expression direction applieddmsa_plot_probes
Panel 1: dense arm against sparse arm, every systemdmsa_plot_systems
Load a gene-to-system polarity tabledmsa_polarity
Validate a candidate polarity tabledmsa_polarity_check
Draft polarity signs for a panel from public databasesdmsa_polarity_fetch
Polarity table for one system, in the form dmsa_align() wantsdmsa_polarity_for
Rows of a polarity table that need a human decisiondmsa_polarity_review
Which public resources DMSA can draft polarity from, and what each is good fordmsa_polarity_sources
Write a template script that fetches probe coordinates from Bioconductordmsa_probe_annotation_template
Probe genomic coordinates, without Bioconductordmsa_probe_coords
Construct a DMSA reference bundledmsa_reference
Read a user-supplied system / module / gene csv as a reference bundledmsa_reference_csv
Read a reference bundle from CSV filesdmsa_reference_read
Write a template csv for a user-supplied referencedmsa_reference_template
Write a reference bundle to a directorydmsa_reference_write
Outcome-free reliability weights for aligned probesdmsa_relweights
Run a declared frame and deliver figures, tables and a summarydmsa_report
Build the whole report: panel 1 once, panels 2 and 3 per firing systemdmsa_report_panels
Save the probes a frame actually analyses, annotated, as a CSVdmsa_save_analysis_set
Subject-level aligned tone scoredmsa_score
Aligned set scores, and the alternatives worth comparing againstdmsa_scores
Split a SummarizedExperiment into the pieces DMSA testsdmsa_se
Select a set of units from a cascadedmsa_select
Load a selection cascade (system > module > gene > probe)dmsa_sets
Validate a candidate cascade before using itdmsa_sets_check
Write a cascade template and the instructions for building onedmsa_sets_template
The systems available in a cascade, with the short names to select them bydmsa_systems
Fixed-sign or expected-sign DMSA pooled testdmsa_test
Re-run the frame's test drivedmsa_test_drive
Build a cascade tree for a set of probes from a reference bundledmsa_tree
Three complementary lenses on the same familydmsa_triangulate
Save a coordinate table so the lookup never has to be repeateddmsa_write_coords