Supplemental Files for manuscript "Prenatal Transmission of Bacteriophage DNA in Humans"

This repository includes the following files:

1) Maternal_UCB_Phage_Analysis.RMDThis is an R markdown file to reproduce the analysis in the manuscript “Prenatal Transmission of Bacteriophage DNA in Humans”.  It depends on the following files:

2) BLAST_Processing.RR script used for the processing of BLAST outputs.  The outputs of this analysis for our two cohorts and negative controls with each phage database are provided as R objects.   a. POPE_AllPhage_Stats.RDS b. POPE_GPD_Stats.RDS c. Witt_AllPhage_Stats.RDS d. Witt_GPD_Stats.RDS e. Neg_AllPhage_Stats.RDS f. Neg_GPD_Stats.RDS

3) Clean_Data_Structures.RThis script includes 3 sections to generate the data structures used in subsequent analyses. 

4) Phage_Plots_Tables.RThis script includes 3 sections to reproduce the figures and tables from the manuscript “Prenatal Transmission of Bacteriophage DNA in Humans”. 

5) POPE_index.csvThis CSV file contains the metadata for the POPE cohort.

6) SummaryMetaData.csvThis CSV file contains the metadata for the Witt cohort as relayed by the study authors from the original publication of this dataset.

7) README.txt which summarizes the above as well as provides links to other relevant data.

These scripts can be used to re-process our sequencing data or to process and interpret additional datasets.