CuratedMetagenomicData Query for Enterocloster spp. and ucd Genes

R code (.R), RData (.RData), and .csv files related to the analysis of curatedMetagenomicData datasets (https://waldronlab.io/curatedMetagenomicData/). The purpose of this analysis was to assess the prevalence of Enterocloster spp. capable of metabolizing urolithin C in human stool metagenomic sequencing experiments (https://waldronlab.io/curatedMetagenomicData/articles/available-studies.html). 

The data were generated/analyzed in the following way:

1 - 1_ExperimentHub_Local_Cache_Export.R was used to generate .RData files for all 93 studies are available in curatedMetagenomicData. The resulting files (.RData) generated are named according to the following convention: Studies##-##.RData.

2 - The Studies##-##.RData files were loaded into an R environment in the Narval compute cluster (Digital Research Alliance of Canada) and the 2_cMD_FromRData.R script was used to query the relative abundance (ra) of bacteria of interest (boi) and the gene families abundance (gf) for genes of interest (goi). Metadata (md) was also extracted from each study. The resulting files (.csv) generated are named according to the following convention: Study##_datatype.csv (datatype = ra_boi, gf_goi, md).

3 - The Study##_datatype.csv (datatype = ra_boi, gf_goi, md) files were then analyzed using the 3_cMD_Merge_Outputs_And_Graph.R script to merge individual outputs into a single dataframe to then graph the prevalence results. The .RData generated throughout the running of this script are provided as cMD_Merge_Outputs_And_Graph.RData

Dependencies for each R script are provided at the start of each script. To reproduce the analysis, file paths must be changed.

The cMD_study_summary.csv file contains metadata related to each study (86 total) included in the analysis.

The cMD_metadata_ra_boi_gf_goi_stool.csv file contains a merged table of sample metadata (n = 21030 samples), relative abundance (ra) for bacteria of interest (boi), gene family (gf) abundance for genes of interest (goi).