Last updated: 2024-06-18
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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 |
| Rmd | fc1ba67 | Michael S. Zens | 2024-06-13 | filled out covariate analysis |
| html | fc1ba67 | Michael S. Zens | 2024-06-13 | filled out covariate analysis |
| Rmd | 0b8b963 | Michael S. Zens | 2024-06-10 | first attempt - dbscan clustering of UMAP |
| html | 50edc75 | Jie Zhou | 2024-06-09 | remove ap data from manuscript1 and remove elisa data from manuscript2 |
| html | 59a1721 | Jie Zhou | 2024-06-08 | added back the case of 4 clusters |
| html | 8c46744 | Jie Zhou | 2024-06-03 | remove antigen elisa |
| html | 70d404c | Jie Zhou | 2024-05-31 | start manuscript 2 |
| Rmd | 62b4a5f | Jie Zhou | 2024-05-31 | start manuscript 2 |
| html | 62b4a5f | Jie Zhou | 2024-05-31 | start manuscript 2 |
| Rmd | 2fd12dc | Jie Zhou | 2024-05-31 | start manuscript 2 |
| html | 2fd12dc | Jie Zhou | 2024-05-31 | start manuscript 2 |
| Rmd | 049442a | Michael S. Zens | 2024-05-21 | Added extreme value assessment |
| html | 049442a | Michael S. Zens | 2024-05-21 | Added extreme value assessment |
| Rmd | ace1261 | Michael S. Zens | 2024-05-14 | addressed a tanglex merge conflict |
| html | ace1261 | Michael S. Zens | 2024-05-14 | addressed a tanglex merge conflict |
| Rmd | e5ce6e8 | Michael S. Zens | 2024-05-14 | fixed confounder tables and PCA function to adjust for confounders |
| html | e5ce6e8 | Michael S. Zens | 2024-05-14 | fixed confounder tables and PCA function to adjust for confounders |
| Rmd | 151b34f | Jie Zhou | 2024-05-13 | conflict |
| html | 151b34f | Jie Zhou | 2024-05-13 | conflict |
| Rmd | 1b36bb0 | Jie Zhou | 2024-05-13 | added the first apwp results |
| html | 1b36bb0 | Jie Zhou | 2024-05-13 | added the first apwp results |
| Rmd | 90c14c7 | Michael S. Zens | 2024-05-08 | Merge branch ‘main’ of git.dartmouth.edu:madi-biostat-group/madi-brussels-pertussis-thailand |
| Rmd | 632c421 | Michael S. Zens | 2024-05-08 | added standard diff |
| html | 632c421 | Michael S. Zens | 2024-05-08 | added standard diff |
| Rmd | 08c7627 | David Kook | 2024-05-08 | feature clustering for unstandardized assay difference between boosted and vaccinated visits |
| Rmd | 1f16e5e | Michael S. Zens | 2024-05-01 | added sections for standardizing across visits and added box plots. |
| html | 1f16e5e | Michael S. Zens | 2024-05-01 | added sections for standardizing across visits and added box plots. |
| html | f3a22c2 | Jie Zhou | 2024-04-28 | update index |
| Rmd | 0b6e118 | Jie Zhou | 2024-04-28 | pulled from gitlab |
| html | 0b6e118 | Jie Zhou | 2024-04-28 | pulled from gitlab |
| Rmd | 42c1edc | Jie Zhou | 2024-04-28 | double pca |
| html | 42c1edc | Jie Zhou | 2024-04-28 | double pca |
| Rmd | c15cd8c | Michael S. Zens | 2024-04-24 | expanded set of ap-wp analyses following David and Lisa |
| html | c15cd8c | Michael S. Zens | 2024-04-24 | expanded set of ap-wp analyses following David and Lisa |
| Rmd | c29bc10 | Michael S. Zens | 2024-04-23 | clusters > 4 |
| html | c29bc10 | Michael S. Zens | 2024-04-23 | clusters > 4 |
| Rmd | 571f572 | Michael S. Zens | 2024-04-10 | changes before meeting |
| html | 9faeda4 | Michael S. Zens | 2024-04-09 | index.html |
| Rmd | adc2fd9 | Michael S. Zens | 2024-04-09 | tried without index and connection |
| Rmd | c79c418 | Michael S. Zens | 2024-04-09 | changes to feature clusters, igg standardization and connection |
| html | c79c418 | Michael S. Zens | 2024-04-09 | changes to feature clusters, igg standardization and connection |
| Rmd | 17ca781 | Jie Zhou | 2024-04-07 | cleanup |
| html | 17ca781 | Jie Zhou | 2024-04-07 | cleanup |
| Rmd | 3b23ab9 | Jie Zhou | 2024-03-25 | added mediation |
| html | 3b23ab9 | Jie Zhou | 2024-03-25 | added mediation |
| Rmd | 8402a16 | Jie Zhou | 2024-03-25 | pulled first |
| html | 8402a16 | Jie Zhou | 2024-03-25 | pulled first |
| Rmd | cfa1fdf | Jie Zhou | 2024-03-25 | index |
| html | cfa1fdf | Jie Zhou | 2024-03-25 | index |
| html | 85f9a78 | Michael S. Zens | 2024-03-06 | added the standardization section to home |
| Rmd | 695b291 | Michael S. Zens | 2024-03-06 | added a revision to the igg standardization |
| Rmd | 2a9bc5d | Michael S. Zens | 2024-03-01 | made index.html |
| html | 2a9bc5d | Michael S. Zens | 2024-03-01 | made index.html |
| Rmd | 931e833 | Michael S. Zens | 2024-03-01 | set update for standardization |
| html | 931e833 | Michael S. Zens | 2024-03-01 | set update for standardization |
| html | 1c55292 | Jie Zhou | 2024-02-22 | for 2/22 Thursday meeting |
| Rmd | 57b63d1 | Jie Zhou | 2024-02-21 | changed the title |
| html | 57b63d1 | Jie Zhou | 2024-02-21 | changed the title |
| Rmd | c4c9d56 | Jie Zhou | 2024-02-21 | pull |
| html | c4c9d56 | Jie Zhou | 2024-02-21 | pull |
| Rmd | 532d320 | Jie Zhou | 2024-02-21 | madi meeting |
| html | 532d320 | Jie Zhou | 2024-02-21 | madi meeting |
| Rmd | f35b00b | Michael S. Zens | 2024-01-31 | big changes to loop_pca and cluster features. |
| html | f35b00b | Michael S. Zens | 2024-01-31 | big changes to loop_pca and cluster features. |
| Rmd | 528d126 | Jie Zhou | 2024-01-23 | added pls and pca based mediation analysis |
| html | 528d126 | Jie Zhou | 2024-01-23 | added pls and pca based mediation analysis |
| Rmd | 7e12be2 | Jie Zhou | 2024-01-15 | added pls mediation analysis |
| html | 7e12be2 | Jie Zhou | 2024-01-15 | added pls mediation analysis |
| Rmd | 3459d5b | Jie Zhou | 2024-01-13 | added pls mediation |
| html | 3459d5b | Jie Zhou | 2024-01-13 | added pls mediation |
| Rmd | 30792a7 | Jie Zhou | 2024-01-13 | added pls mediation analysis |
| html | 30792a7 | Jie Zhou | 2024-01-13 | added pls mediation analysis |
| Rmd | c5d3005 | Michael S. Zens | 2024-01-03 | manual merge of index.Rmd |
| html | c5d3005 | Michael S. Zens | 2024-01-03 | manual merge of index.Rmd |
| Rmd | 9f68a29 | Michael S. Zens | 2024-01-03 | converted to better looping and markdown control |
| html | 9f68a29 | Michael S. Zens | 2024-01-03 | converted to better looping and markdown control |
| Rmd | 064251e | Jie Zhou | 2023-12-17 | added data folder |
| html | 064251e | Jie Zhou | 2023-12-17 | added data folder |
| html | a7ae2fc | Jie Zhou | 2023-12-17 | pulled from gitlab |
| html | 3689df3 | Jie Zhou | 2023-12-17 | update? |
| Rmd | 029670b | Michael S. Zens | 2023-12-07 | added part cor to the dimension reduction |
| html | 029670b | Michael S. Zens | 2023-12-07 | added part cor to the dimension reduction |
| html | 6ddb074 | Jie Zhou | 2023-12-06 | render index file |
| html | 824148d | Jie Zhou | 2023-12-06 | resolve confict |
| html | 394c867 | Jie Zhou | 2023-12-06 | volcano plots |
| html | 3efee73 | Jie Zhou | 2023-12-06 | revised volcano |
| html | b99d1b7 | Michael S. Zens | 2023-12-05 | second pass on the committing dimension reduction |
| Rmd | 5326207 | Michael S. Zens | 2023-12-05 | Near completed Dimension reduction PCA R markdown |
| html | 5326207 | Michael S. Zens | 2023-12-05 | Near completed Dimension reduction PCA R markdown |
| html | 30b0f4b | Jie Zhou | 2023-12-05 | re knit the files |
| html | 1b91eb7 | Jie Zhou | 2023-12-05 | same antigen for outcome and mediators |
| html | 94f6550 | Jie Zhou | 2023-12-05 | update index |
| html | 43d9f5b | Jie Zhou | 2023-12-05 | revised mediation analysis |
| Rmd | 97298f8 | Michael S. Zens | 2023-12-05 | modfied the workflowr with better summaries |
| html | 97298f8 | Michael S. Zens | 2023-12-05 | modfied the workflowr with better summaries |
| Rmd | ce5706a | Michael S. Zens | 2023-12-04 | adjusted the index file slightly |
| html | ce5706a | Michael S. Zens | 2023-12-04 | adjusted the index file slightly |
| Rmd | d377706 | Michael S. Zens | 2023-12-04 | Merge branch ‘main’ of git.dartmouth.edu:madi-biostat-group/madi-brussels-pertussis-thailand |
| Rmd | 3d7325b | Michael S. Zens | 2023-12-04 | added the pca to the workflowr |
| Rmd | 24b5b34 | Jie Zhou | 2023-12-04 | added updated index |
| html | 24b5b34 | Jie Zhou | 2023-12-04 | added updated index |
| Rmd | 815d630 | Jie Zhou | 2023-12-04 | pull results |
| html | 815d630 | Jie Zhou | 2023-12-04 | pull results |
| Rmd | a6c659b | Jie Zhou | 2023-12-04 | revised the mediation |
| html | a6c659b | Jie Zhou | 2023-12-04 | revised the mediation |
| html | a0cc642 | Michael S. Zens | 2023-12-04 | trying to push index changes |
| Rmd | 7dd7701 | Michael S. Zens | 2023-12-04 | working on the main index page: |
| html | 7dd7701 | Michael S. Zens | 2023-12-04 | working on the main index page: |
| Rmd | 9704b73 | Jie Zhou | 2023-12-04 | edit index file |
| html | 9704b73 | Jie Zhou | 2023-12-04 | edit index file |
| html | f793b0d | Jie Zhou | 2023-12-04 | pull new updates |
| html | b500aeb | Michael S. Zens | 2023-12-04 | working on the workflowr |
| Rmd | 3735360 | Michael S. Zens | 2023-12-04 | fixed the table of contents; updated the clustering for review |
| Rmd | 31edbec | Michael S. Zens | 2023-12-03 | working on updating the workflowr parts |
| html | 94b74b8 | Jie Zhou | 2023-12-01 | ready for mediation |
| html | 8b66100 | Michael S. Zens | 2023-11-06 | added a connection.R chunk of code to code/ and made reference to in it on .Rmd |
| Rmd | a40c7c8 | Michael S. Zens | 2023-11-06 | added workflowr parts |
Summary:
Welcome to an analysis of infant immune response to maternal and infant immunization.
This cohort study (ClinicalTrials.gov NCT02408926) of paired mothers and infants have been recruited in Thailand to assess
the effect of pertussis maternal immunization on the infant pertussis vaccine response, and
to compare the interference of pertussis maternal immunization upon infant pertussis vaccination with either a tetanus and diphtheria combined pertussis whole-cell (DTwP abbr. wP) or acellular vaccine (DTaP abbr. aP).
The factors [IgG total, IgG1, IgG2, IgG3, IgG4, FcgR2a, FcgR3b, ADCP, ADNP, ADCD] may influence the baseline immunological status of the infant and therefore influence its own vaccine responses. All these parameters are collected or measured in mothers at recruitment and at delivery and in children during early life.
The measured outcomes are antigen specific and the assays are composed of 7 antigens: 3 pertussis vaccine antigens (pertussis toxin PT, filamentous hemagglutinin FHA, pertactin PRN), 2 non-pertussis vaccine antigens (diphtheria toxin DT, tetanus toxin TT) and 2 non vaccine antigens (pentamer, glycoprotein B gB from CMV).
The study is focused on pertussis responses but we also include antigens that are also components of the aP or wP vaccines to evaluate a potential impact on them. The CMV antigens are used as controlled antigens, not supposed to vary with pertussis vaccination.
Specific dilutions were selected for each analyte across planned visits and antigens.