Data and analysis supporting “Aberrant newborn T cell and microbiota developmental trajectories predict respiratory compromise during infancy.” Preprint
- data: minimally processed data – microbiome OTU counts, T cell subpopulation abundances, subject covariates, etc
- intermediates: derived tables and output from scripts
To reproduce some results, data will need to be downloaded from
dbGAP,
as some data posted here has been jittered, quantized or redacted to
reduce the risk of reidentification of subjects. The Alias key will
join subject-level tables to data in dbGAP.
- 01_make_cst: Run DMN model on OTU and flowsom metaclusters and find best-fitting model
- 01_table1_demographics: Summarize some demographic variables to generate portions of “table 1” in the paper.
- 02_network_modeling: Test for pairwise associations between CST, IST and flowsom metacluster
- 02_ist_cst_results: Heatmaps of IST/CST composition, associations with gestational age and postmenstrual age
- 03_development_index: prediction of PMA from microbiome and T cell subpopulations. Developmental index. Prediction of PRD.
- 04_multivariate_r2: Estimates of variance explained from microbiome vs T cells, adjusting for term and PMA (figure 1)
- 04_tcell_associations PMA associations of T cell cluster abundance and broken-stick regression models of the same. CMV/Inflammation associations between IST.
- flowcytometry: scripts for processing T cell flow cytometry (TPHE/ICS) to produce flowsom “metacluster” populations. FCS files would need to be downloaded from IMMPORT to run these scripts.
These don’t necessarily need to be run in order, as their inputs have
been saved under intermediates.
To install all dependencies run devtools::install(CoordinatedTDeps, lib = <some new directory>) where you may wish to set <some new directory> to be a path besides your default .libPaths() to keep
these packages isolated.
Run using R 3.5.1 and Bioconductor 3.7, and YMMV otherwise.
devtools::load_all('CoordinatedTDeps')## Loading CoordinatedTDeps
devtools::session_info()## Session info ------------------------------------------------------------------
## setting value
## version R version 3.5.1 (2018-07-02)
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz America/New_York
## date 2020-07-14
## Packages ----------------------------------------------------------------------
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