Data Analysis for Maternal-infant Vaccination

Infant immunization for pertussis: AP vs. WP

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Last updated: 2024-10-16

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Knit directory: MADI-Project3-SDY8003-Thailand/

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File	Version	Author	Date	Message
html	dda6b8f	f006zvn1	2024-10-16	changed index pages
html	51547b5	f006zvn1	2024-10-16	changed index pages
Rmd	7754f6d	f006zvn1	2024-10-16	changed index pages
Rmd	b797383	Michael S. Zens	2024-10-03	latest sets of feature estimates and plots.
Rmd	2ab8fdd	Michael S. Zens	2024-09-16	added feature_comparisions and fixed the deimension reduction for 6 variations of clustering for each manuscript.
Rmd	d0f0c4a	Michael S. Zens	2024-09-12	cleaned up clustering analysis codes
Rmd	30d4812	Michael S. Zens	2024-09-09	commit merge_fixed_v1
html	b2b32c1	Michael S. Zens	2024-09-09	commiting html files that I wish I could forget.
Rmd	e1a0085	Michael S. Zens	2024-09-09	msz changes for clustering and tanglegrams
Rmd	a0b7381	Jie Zhou-2	2024-08-17	remove mediation analysis for apwp
html	a0b7381	Jie Zhou-2	2024-08-17	remove mediation analysis for apwp
html	a60ab45	Jie Zhou-2	2024-08-14	added mixed effects model
html	f517c3a	Jie Zhou-2	2024-08-06	added sex to the mediation model
html	fe5a646	Jie Zhou-2	2024-08-05	fix the conflicts
html	a4226da	Jie Zhou-2	2024-08-05	added vifBasedSelection.R
html	c8d0708	Kookd	2024-07-30	umap for apwp 6 clusters didn’t look right
html	573d7bd	Kookd	2024-07-29	updating wiki docs to reflect updated umap
html	d6b37f1	Kookd	2024-07-29	updated index html files
Rmd	e0dfe6d	Kookd	2024-07-29	cluster features by arm for apwp and matim+/-, for 6 and 7 clusters. updated wiki-related documents
Rmd	ab9b91f	Michael S. Zens	2024-06-18	big set of maternal Tdap+ vs Tdap- results
html	ab9b91f	Michael S. Zens	2024-06-18	big set of maternal Tdap+ vs Tdap- results

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Summary:

Welcome to an analysis of infant immune response to maternal and infant immunization.

• All analyses presented on this page are for examining the difference between infants receiving the AP and WP vaccines.

1 Outlier and Anomaly detection by feature

1. Review assay responses and extreme values for imputation or exclusion

2. Review PCA and UMAP projection of all antigens and features by arm

2 IgG standardization

1. Check ELISA total IgG correlation with bead array MFI total IgG
2. Standardization regression - by antigen, feature and visit
3. Summary across all features - IgG Standardization - by antigen, feature and visit
4. JIVE Decomposition Between IgG, FcR and Effector Function Data

3 Individual feature analysis - Study arm and covariates

1. Comparisons by feature and visit - unstandardized and standardized
2. Summary by visit - unstandardized and standardized forest and volcano plots

4 Feature Clustering

• In the Feature Clustering section, all features reflecting antibody and functional analytes binding to five antigens at the vaccinated (Month 7) and boosted (Month 19) time points are examined to determine clusters of associated features that will be response variables for the analysis.

1. Vaccinated and Boosted: unstandardized features - 7 clusters

2. Vaccinated and Boosted: standardized features by total IgG - 7 clusters

3. Vaccinated and Boosted: standardized features by total IgG - 7 clusters_no IgG

4. Vaccinated and Boosted: unstandardized features - 6 clusters

5. Vaccinated and Boosted: standardized features by total IgG - 6 clusters

6. Vaccinated and Boosted: standardized features by total IgG - 6 clusters - noIgG

7. by Arm and visit - include total IgG: not standardized - 7 clusters

8. by Arm and Visit - include total IgG: standardized - 7 clusters

9. by Arm and visit - exclude total IgG: not standardized - 7 clusters

10. by Arm and Visit - exclude total IgG: standardized - 7 clusters

11. by Arm and Visit - exclude total IgG: standardized - 6 clusters

5 Dimension Reduction and Confounding

• In the Dimension Reduction section, principle components are calculated for the pertussis related antigens (PT, FHA, PRN), other infant strains (DT, TT), and each of the Feature Clusters identified at the vaccinated and boosted time points.

  1. Table 1. Covariates associate with Study Arm

  2. Antigen & Unsupervised clusters: Not standardized - excluding ELISA total IgG - 7 clusters

  3. Antigen & Unsupervised clusters: Total IgG standardized - excluding ELISA total IgG - 7 clusters

  4. Antigen & Unsupervised clusters: Total IgG standardized - all total IgG - 7 clusters

  5. Antigen & Unsupervised clusters: Not standardized - excluding ELISA total IgG - 6 clusters

  6. Antigen & Unsupervised clusters: Total IgG standardized - excluding ELISA total IgG - 6 clusters

  7. Antigen & Unsupervised clusters: Total IgG standardized - all total IgG - 6 clusters

  8. Summary - Antigen & Unsupervised clusters associated with covariates

6 Causal Mediation Analysis

• In the Causal Mediation Analysis section, the direct effects of the study treatments may be mediated by Cord blood (at birth) total IgG or Prevaccinated infant serum (Month 2). Response variables are of three types.

1. mediator: maternal serum, response: infant age 7 mo. (vaccinated,apwp)