R version 4.2.2 (2022-10-31) or higher
randomForestSRC version 3.2.1
gplots veresion 3.1.3
When used in concert with the vaginal non-redundant gene database (VIRGO), assigns metagenomic community state types (mgCSTs) to vaginal metagenomes. This script requires VIRGO output files "summary.Abundance.txt" and "summary.NR.abundance.txt" as well as VIRGO reference file 0.geneLength.txt.
- Clone this repository
- Run data through VIRGO (https://virgo.igs.umaryland.edu).
- Download the metagenomic subspecies random forest classifier from https://figshare.com/ndownloader/files/36123449 and place in the github repository directory.
- Run classifier. The classifier will first assign metagenomic subspecies using the mgss_classifier.RDS file downloaded from figshare. It will then assign metagenomic CSTs to each sample using a nearest-neighbor, centroid-based classifier.
Full paths to the following files/directories must be supplied in this order:
(1) summary.Abundance.txt
(2) summary.NR.abundance.txt
(3) VIRGO-master directory
(4) mgCST-classifier-master directory
Example:
Rscript classify_mgCST_centroid.R example/summary.Abundance.txt example/summary.NR.abundance.txt /full/path/to/VIRGO-master /full/path/to/mgCST-classifier-master
Output is written to current directory. Each output file is dated.
Output files:
relabund_w_mgCSTs_1Jul2022.csv: Relative abundances of metagenomic subspecies (columns) by samples (rows). Right-most column contains mgCST classification.
mgCST_heatmap_1Jul2022.pdf: A heatmap of relative abundances of 50 most abundant metagenomic subspecies with samples colored by mgCST.
mgCSTs_1Jul2022.csv: Two-column table with sample ID and mgCST assignment
norm_counts_mgSs_mgCST_1Jul2022.csv: Gene abundances normalized by gene length of metagenomic subspecies (columns) by samples (rows). Right-most column contains mgCST classification.