JIVE AP vs. WP
Alec Buetow
2024-10-14
Last updated: 2024-11-25
Checks: 7 0
Knit directory:
madi-biostat-project3-SDY8003-Thailand/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | f00f669 | alecbuetow | 2024-11-25 | explained why JIVE picks # ranks |
| html | f00f669 | alecbuetow | 2024-11-25 | explained why JIVE picks # ranks |
| html | 69c2601 | alecbuetow | 2024-11-20 | corrected duplicate JIVE |
| Rmd | 9f50e73 | alecbuetow | 2024-11-20 | more polish |
| Rmd | df305a9 | alecbuetow | 2024-11-20 | polish |
| html | df305a9 | alecbuetow | 2024-11-20 | polish |
| Rmd | 0cc81b6 | alecbuetow | 2024-11-20 | made changes to loading extraction in JIVE and PCA correlation circle: |
| html | 0cc81b6 | alecbuetow | 2024-11-20 | made changes to loading extraction in JIVE and PCA correlation circle: |
| Rmd | 366e256 | alecbuetow | 2024-11-19 | added loading plots to JIVE |
| html | 366e256 | alecbuetow | 2024-11-19 | added loading plots to JIVE |
| Rmd | f3de555 | alecbuetow | 2024-11-12 | many changes |
| Rmd | 65b4e9d | alecbuetow | 2024-11-05 | made fisher test more consistent |
| Rmd | bde08e9 | alecbuetow | 2024-11-04 | Add large file with Git LFS |
| html | bde08e9 | alecbuetow | 2024-11-04 | Add large file with Git LFS |
| Rmd | d6f0da4 | f006zvn1 | 2024-10-29 | saving progress, testing new ssh key |
| html | d6f0da4 | f006zvn1 | 2024-10-29 | saving progress, testing new ssh key |
| Rmd | ea93e22 | f006zvn1 | 2024-10-25 | jive apwp complete |
| html | ea93e22 | f006zvn1 | 2024-10-25 | jive apwp complete |
| Rmd | 4100daf | f006zvn1 | 2024-10-23 | cmv seropositivty added |
| Rmd | b5c2adb | f006zvn1 | 2024-10-22 | restructured standardized vs. unstandardized JIVE |
| html | b5c2adb | f006zvn1 | 2024-10-22 | restructured standardized vs. unstandardized JIVE |
| Rmd | f667132 | f006zvn1 | 2024-10-22 | added standardized data section |
| html | f667132 | f006zvn1 | 2024-10-22 | added standardized data section |
| Rmd | 3eb4ec7 | f006zvn1 | 2024-10-21 | fixed jitter |
| html | 3eb4ec7 | f006zvn1 | 2024-10-21 | fixed jitter |
| Rmd | b70ef48 | f006zvn1 | 2024-10-16 | corrected typos |
| html | b70ef48 | f006zvn1 | 2024-10-16 | corrected typos |
| Rmd | fc9b419 | f006zvn1 | 2024-10-16 | renamed chunks to make pngs neater |
| html | fc9b419 | f006zvn1 | 2024-10-16 | renamed chunks to make pngs neater |
| Rmd | 19a62eb | f006zvn1 | 2024-10-16 | fixed categorical labels |
| html | 19a62eb | f006zvn1 | 2024-10-16 | fixed categorical labels |
| Rmd | 3a356e9 | f006zvn1 | 2024-10-16 | JIVE updated with covariates |
| html | 3a356e9 | f006zvn1 | 2024-10-16 | JIVE updated with covariates |
| Rmd | ae2edc0 | f006zvn1 | 2024-10-16 | JIVE changes |
| html | ae2edc0 | f006zvn1 | 2024-10-16 | JIVE changes |
Dataset
Unstandardized
Joint and Individual Variance Explained (JIVE):
Analytes were categorized into IgG, Fc Receptors, and Effector Functions, with data from each category analyzed using the JIVE algorithm to decompose shared (joint) and unique (individual) variation components.
Matrix Rank (number of pricincipal components selected) was determined by significance testing as part of the JIVE algorithm. Principal components that explained a statistically significant amount of variance at α = 0.05 were retained, while all others were excluded.
Vaccinated
Joint Matrix Rank: 3
Individual Matrices Rank:
IgG: 2
FcR: 1
Effector Functions: 2
Original Matrices Rank:
IgG: 33
FcR: 12
Effector Functions: 16
Variation Explained
Joint PCA
Joint + Individual PCA
PC Loadings
Joint
IgG
FcR
Boosted
Joint Matrix Rank: 1
Individual Matrices Rank:
IgG: 2
FcR: 2
Effector Functions: 1
Original Matrices Rank:
IgG: 33
FcR: 12
Effector Functions: 16
Joint + Individual PCA
Classification Analysis:
Subject classifications were derived from clusters appearing in the JIVE plots above. If no latent clusters were evident, then subject classifications are unavailable.
| Vaccinated vs Boosted Classification | ||
| Below | Above | |
|---|---|---|
| Below | 37 | 0 |
| Above | 9 | 26 |
Vaccinated
| Classification by Arm | ||
| Arm | Classification | Number of Subjects |
|---|---|---|
| maternal Tdap - infant ap | Below | 18 |
| maternal Tdap - infant ap | Above | 18 |
| maternal Tdap - infant ap | NA | 0 |
| maternal Tdap - infant wp | Below | 22 |
| maternal Tdap - infant wp | Above | 19 |
| maternal Tdap - infant wp | NA | 1 |
Subjects who are missing all data within any given domain (IgG, FcR, or Effector) cannot be classified and are marked as NA.
Birth Weight
P-Values are calculated from a two tailed T-Test with no FDR correction.
CMV Seropositivity
| Classification by CMV Seropositivity | ||
| Below | Above | |
|---|---|---|
| No | 0 | 28 |
| Yes | 37 | 7 |
| Unknown | 3 | 2 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Infant Sex
| Classification by Infant Sex | ||
| Below | Above | |
|---|---|---|
| Male | 23 | 19 |
| Female | 17 | 18 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Delivery Mode
| Classification by Delivery Mode | ||
| Below | Above | |
|---|---|---|
| Vaginal | 16 | 14 |
| Caesarian | 24 | 23 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Parity
| Classification by Parity | ||
| Below | Above | |
|---|---|---|
| 0 | 28 | 20 |
| 1 | 7 | 15 |
| 2 | 4 | 2 |
| 3 | 1 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Gravidity
| Classification by Gravidity | ||
| Below | Above | |
|---|---|---|
| 1 | 22 | 18 |
| 2 | 13 | 15 |
| 3 | 3 | 4 |
| 4 | 2 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Gestational Age at Vaccine
P-Values are calculated from a two tailed T-Test with no FDR correction.
Infant Interval Between Vaccination and Delivery Days
P-Values are calculated from a two tailed T-Test with no FDR correction.
Gestational Age at Delivery
P-Values are calculated from a two tailed T-Test with no FDR correction.
Maternal Age at Delivery
P-Values are calculated from a two tailed T-Test with no FDR correction.
IgG
DT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_FHA_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_PRN_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_PT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
FcR
DT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
Effector
DT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
Boosted
| Classification by Arm | ||
| Arm | Classification | Number of Subjects |
|---|---|---|
| maternal Tdap - infant ap | Below | 21 |
| maternal Tdap - infant ap | Above | 14 |
| maternal Tdap - infant ap | NA | 1 |
| maternal Tdap - infant wp | Below | 26 |
| maternal Tdap - infant wp | Above | 12 |
| maternal Tdap - infant wp | NA | 2 |
Subjects who are missing all data within any given domain (IgG, FcR, or Effector) cannot be classified and are marked as NA.
Birth Weight
P-Values are calculated from a two tailed T-Test with no FDR correction.
CMV Seropositivity
| Classification by CMV Seropositivity | ||
| Below | Above | |
|---|---|---|
| No | 2 | 26 |
| Yes | 45 | 0 |
| Unknown | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Infant Sex
| Classification by Infant Sex | ||
| Below | Above | |
|---|---|---|
| Male | 26 | 15 |
| Female | 21 | 11 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Delivery Mode
| Classification by Delivery Mode | ||
| Below | Above | |
|---|---|---|
| Vaginal | 17 | 11 |
| Caesarian | 30 | 15 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Parity
| Classification by Parity | ||
| Below | Above | |
|---|---|---|
| 0 | 29 | 14 |
| 1 | 13 | 10 |
| 2 | 4 | 2 |
| 3 | 1 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Gravidity
| Classification by Gravidity | ||
| Below | Above | |
|---|---|---|
| 1 | 22 | 13 |
| 2 | 19 | 10 |
| 3 | 4 | 3 |
| 4 | 2 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Gestational Age at Vaccine
P-Values are calculated from a two tailed T-Test with no FDR correction.
Infant Interval Between Vaccination and Delivery Days
P-Values are calculated from a two tailed T-Test with no FDR correction.
Gestational Age at Delivery
P-Values are calculated from a two tailed T-Test with no FDR correction.
Maternal Age at Delivery
P-Values are calculated from a two tailed T-Test with no FDR correction.
IgG
DT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_FHA_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_PRN_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_PT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
FcR
DT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
Effector
DT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
Citations:
Michael J. O’Connell, Eric F. Lock, R.JIVE for exploration of multi-source molecular data, Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2877–2879, https://doi.org/10.1093/bioinformatics/btw324
Eric F. Lock, Katherine A. Hoadley, J. S. Marron, Andrew B. Nobel, “Joint and individual variation explained (JIVE) for integrated analysis of multiple data types,” The Annals of Applied Statistics, Ann. Appl. Stat. 7(1), 523-542, (March 2013), https://doi.org/10.1214/12-AOAS597
Standardized by Total IgG
Joint and Individual Variance Explained (JIVE):
Analytes were categorized into IgG, Fc Receptors, and Effector Functions, with data from each category analyzed using the JIVE algorithm to decompose shared (joint) and unique (individual) variation components.
Matrix Rank (number of pricincipal components selected) was determined by significance testing as part of the JIVE algorithm. Principal components that explained a statistically significant amount of variance at α = 0.05 were retained, while all others were excluded.
Vaccinated
Joint Matrix Rank: 2
Individual Matrices Rank:
IgG: 1
FcR: 2
Effector Functions: 1
Original Matrices Rank:
IgG: 33
FcR: 12
Effector Functions: 16
Variation Explained
Joint PCA
Joint + Individual PCA
Boosted
Joint Matrix Rank: 2
Individual Matrices Rank:
IgG: 1
FcR: 1
Effector Functions: 2
Original Matrices Rank:
IgG: 33
FcR: 12
Effector Functions: 16
Variation Explained
Joint PCA
Joint + Individual PCA
Classification Analysis:
Subject classifications were derived from clusters appearing in the JIVE plots above. If no latent clusters were evident, then subject classifications are unavailable.
| Vaccinated vs Boosted Classification | ||
| Below | Above | |
|---|---|---|
| Below | 0 | 0 |
| Above | 0 | 0 |
Vaccinated
Subjects who are missing all data within any given domain (IgG, FcR, or Effector) cannot be classified and are marked as NA.
Birth Weight
P-Values are calculated from a two tailed T-Test with no FDR correction.
CMV Seropositivity
| Classification by CMV Seropositivity | ||
| Below | Above | |
|---|---|---|
| No | 0 | 0 |
| Yes | 0 | 0 |
| Unknown | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Infant Sex
| Classification by Infant Sex | ||
| Below | Above | |
|---|---|---|
| Male | 0 | 0 |
| Female | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Delivery Mode
| Classification by Delivery Mode | ||
| Below | Above | |
|---|---|---|
| Vaginal | 0 | 0 |
| Caesarian | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Parity
| Classification by Parity | ||
| Below | Above | |
|---|---|---|
| 0 | 0 | 0 |
| 1 | 0 | 0 |
| 2 | 0 | 0 |
| 3 | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Gravidity
| Classification by Gravidity | ||
| Below | Above | |
|---|---|---|
| 1 | 0 | 0 |
| 2 | 0 | 0 |
| 3 | 0 | 0 |
| 4 | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Gestational Age at Vaccine
P-Values are calculated from a two tailed T-Test with no FDR correction.
Infant Interval Between Vaccination and Delivery Days
P-Values are calculated from a two tailed T-Test with no FDR correction.
Gestational Age at Delivery
P-Values are calculated from a two tailed T-Test with no FDR correction.
Maternal Age at Delivery
P-Values are calculated from a two tailed T-Test with no FDR correction.
IgG
DT_IgG1
Warning: Using one column matrices in `filter()` was deprecated in dplyr 1.1.0.
ℹ Please use one dimensional logical vectors instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG1
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG2
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG3
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG4
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_FHA_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_PRN_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_PT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG
P-Values are calculated from a two tailed T-Test with no FDR correction.
FcR
DT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_FcgR3b
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_FcgR2a
P-Values are calculated from a two tailed T-Test with no FDR correction.
Effector
DT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADNP
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADCD
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADCP
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADNP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
Boosted
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
Subjects who are missing all data within any given domain (IgG, FcR, or Effector) cannot be classified and are marked as NA.
Birth Weight
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
CMV Seropositivity
| Classification by CMV Seropositivity | ||
| Below | Above | |
|---|---|---|
| No | 0 | 0 |
| Yes | 0 | 0 |
| Unknown | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Infant Sex
| Classification by Infant Sex | ||
| Below | Above | |
|---|---|---|
| Male | 0 | 0 |
| Female | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Delivery Mode
| Classification by Delivery Mode | ||
| Below | Above | |
|---|---|---|
| Vaginal | 0 | 0 |
| Caesarian | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Parity
| Classification by Parity | ||
| Below | Above | |
|---|---|---|
| 0 | 0 | 0 |
| 1 | 0 | 0 |
| 2 | 0 | 0 |
| 3 | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Gravidity
| Classification by Gravidity | ||
| Below | Above | |
|---|---|---|
| 1 | 0 | 0 |
| 2 | 0 | 0 |
| 3 | 0 | 0 |
| 4 | 0 | 0 |
P-Values are calculated from Fisher’s Exact Test with no FDR correction.
Gestational Age at Vaccine
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
Infant Interval Between Vaccination and Delivery Days
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
Gestational Age at Delivery
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
Maternal Age at Delivery
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
IgG
DT_IgG1
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG2
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG3
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG4
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG1
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG2
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG3
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG4
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG1
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG2
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG3
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG4
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG1
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG2
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG3
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG4
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG1
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG2
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG3
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG4
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG1
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG2
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG3
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG4
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_FHA_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_PRN_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
ELISA_PT_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_IgG
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FcR
DT_FcgR2a
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_FcgR3b
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_FcgR2a
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_FcgR3b
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_FcgR2a
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_FcgR3b
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_FcgR2a
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_FcgR3b
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_FcgR2a
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_FcgR3b
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_FcgR2a
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_FcgR3b
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
Effector
DT_ADCD
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_ADCP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
DT_ADNP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADCD
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADCP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
FHA_ADNP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
gB_ADCD
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADCD
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADCP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PRN_ADNP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADCD
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADCP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
PT_ADNP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADCD
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADCP
| Version | Author | Date |
|---|---|---|
| f667132 | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
TT_ADNP
| Version | Author | Date |
|---|---|---|
| b5c2adb | f006zvn1 | 2024-10-22 |
P-Values are calculated from a two tailed T-Test with no FDR correction.
Citations:
Michael J. O’Connell, Eric F. Lock, R.JIVE for exploration of multi-source molecular data, Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2877–2879, https://doi.org/10.1093/bioinformatics/btw324
Eric F. Lock, Katherine A. Hoadley, J. S. Marron, Andrew B. Nobel, “Joint and individual variation explained (JIVE) for integrated analysis of multiple data types,” The Annals of Applied Statistics, Ann. Appl. Stat. 7(1), 523-542, (March 2013), https://doi.org/10.1214/12-AOAS597
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.1.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] broom_1.0.7 e1071_1.7-16 glue_1.8.0 RPostgres_1.4.7
[5] DT_0.33 data.table_1.16.2 DBI_1.2.3 RColorBrewer_1.1-3
[9] ggforce_0.4.2 ggpubr_0.6.0 gt_0.11.1 knitr_1.48.1
[13] here_1.0.1 magrittr_2.0.3 r.jive_2.4 lubridate_1.9.3
[17] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[21] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1
[25] tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 farver_2.1.2 blob_1.2.4 bitops_1.0-9
[5] fastmap_1.2.0 tweenr_2.0.3 promises_1.3.0 digest_0.6.37
[9] timechange_0.3.0 lifecycle_1.0.4 compiler_4.4.2 rlang_1.1.4
[13] sass_0.4.9 tools_4.4.2 utf8_1.2.4 yaml_2.3.10
[17] ggsignif_0.6.4 labeling_0.4.3 htmlwidgets_1.6.4 bit_4.5.0
[21] plyr_1.8.9 xml2_1.3.6 abind_1.4-8 KernSmooth_2.23-24
[25] workflowr_1.7.1 withr_3.0.1 grid_4.4.2 polyclip_1.10-7
[29] fansi_1.0.6 git2r_0.33.0 caTools_1.18.3 colorspace_2.1-1
[33] scales_1.3.0 gtools_3.9.5 MASS_7.3-61 cli_3.6.3
[37] crayon_1.5.3 rmarkdown_2.28 generics_0.1.3 rstudioapi_0.16.0
[41] reshape2_1.4.4 tzdb_0.4.0 commonmark_1.9.2 proxy_0.4-27
[45] cachem_1.1.0 vctrs_0.6.5 jsonlite_1.8.9 carData_3.0-5
[49] car_3.1-3 hms_1.1.3 bit64_4.5.2 rstatix_0.7.2
[53] Formula_1.2-5 jquerylib_0.1.4 stringi_1.8.4 gtable_0.3.5
[57] later_1.3.2 munsell_0.5.1 pillar_1.9.0 htmltools_0.5.8.1
[61] gplots_3.2.0 R6_2.5.1 rprojroot_2.0.4 evaluate_1.0.1
[65] markdown_1.13 highr_0.11 backports_1.5.0 httpuv_1.6.15
[69] bslib_0.8.0 class_7.3-22 Rcpp_1.0.13 whisker_0.4.1
[73] xfun_0.48 fs_1.6.4 pkgconfig_2.0.3