Microbial Ecological Instability And Non-Linear Host Interactions Shape Airway Inflammation In HIV-Associated COPD.
Authors/Creators
-
1.
Makerere University
- 2. Makerere University Lung Institute
-
3.
Max Delbrück Center
- 4. Max Delbrück Centrum für Molekulare Medizin Experimental and Clinical Research Center
Description
COPD / HIV BAL Microbiome–Transcriptome Analysis
Analysis code and processed-data inputs for the manuscript. This README lists
what is in the repository, what each file is for, and where to find it.
Scripts (R/)
Run in numeric order — later scripts use objects and files produced by earlier ones.
|
File |
What it is / does |
|
00_prep.R |
Loads and cleans sample metadata; builds the metadata object used by all downstream scripts |
|
01_diversity.R |
Alpha/beta diversity, PERMANOVA, diversity figure panels (Fig 3) |
|
02_genera.R |
Per-genus relative-abundance mixed models (visite × DualStatus) |
|
03_batch_correction.R |
Sentinel-control batch/drift correction; writes the bloomer/decreaser genus scores |
|
04_genus_cell_LM.R |
CLR-transformed genus × cell-fraction linear models |
|
05_RNA_associations.R |
DESeq2 VST, KEGG enrichment, RNA association figure panels |
|
06_linear_models.R |
Gene–microbe linear models with confounder adjustment |
|
07_metadeconf.R |
MetaDeconfoundR on the full cohort |
|
08_metadeconf_HIVpos.R |
Stratified MetaDeconfoundR (HIV+/COPD strata) |
|
09_lung_variables.R |
Delta lung-function models |
|
utils_ggsave.R |
Plotting/export helper, sourced by the figure scripts (not run standalone) |
Processed-data inputs (data/)
These are the actual inputs the scripts read. Files originally saved with a
.r extension are binary R objects (load with readRDS()), renamed to .rds.
|
File |
What it is |
Used by |
|
1224_Samp_data.csv |
Sample metadata table |
00 |
|
rarefied_filtered_relAb_genus.rds |
Genus relative abundance; loads via readRDS() |
01, 02 |
|
rarefied_filtered_relAb_otu.rds |
OTU relative abundance; loads via readRDS() |
01 |
|
rarefied_filtered_relAb_phylum.rds |
Phylum relative abundance; loads via readRDS() |
01 |
|
rarefied_filtered_raw_reads_genus.rds |
Raw rarefied genus reads; loads via readRDS() |
01, 03 |
|
rarefied_filtered_raw_reads_otu.rds |
Raw rarefied OTU reads; loads via readRDS() |
01 |
|
rarefied_filtered_raw_reads_phylum.rds |
Raw rarefied phylum reads; loads via readRDS() |
01 |
|
genus_OTU_mapping.tsv |
Genus ↔ OTU lookup |
01, 02 |
|
df_wide_genus_withscores.rds |
Genus table with batch scores (output of 03, kept so 01 runs standalone); loads via readRDS() |
01 |
|
counDubliClust_82samples.rds |
RNA count matrix (object counDubliClust); loads via readRDS() |
05 |
|
colData11624.rds |
RNA/sample colData (object colData); loads via readRDS() |
05, 07, 08 |
|
normalized_logcpm_tmm.rds |
TMM-normalised logCPM; loads via readRDS() |
06 |
|
25820_normalized_nonlog_cpm.csv |
Non-log CPM |
06 |
|
combined_raw_long_cytofCorrected.rds |
CyTOF cell-fraction long table; loads via readRDS() |
04, 07 |
|
cell_type_props_all_metadata.csv |
Cell-type proportions with metadata |
04 |
Outputs (output/)
Generated by the scripts — figures and result tables (model_results_*,
aic_*, cca_*, permanova_*, anova_*). These are produced, not inputs,
and are written here when the scripts run.
Where to find things at a glance
-
Analysis code → R/
-
Data the scripts read → data/
-
Results the scripts write → output/
-
Not included: result tables are outputs, so they live in output/ after a
run and are not committed as inputs.