R/TCGA.contaminants.R

In twbattaglia/MicrobeDS: Microbiome Datasets

#' @title The Cancer Genome Atlas (TCGA) contaminant list
#' @details WGS unampped reads with Kraken2 profiling from primary tumors
#' @description The Cancer Genome Atlas (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads
#' @usage data('TCGA')
#' @docType data
#' @source ftp://ftp.microbio.me/pub/cancer_microbiome_analysis
#' @format An object of class \code{"phyloseq"}.
#' @keywords datasets
#' @references Poore  et al. (2020) Nature Mar;579(7800):567-574
#' (\href{https://pubmed.ncbi.nlm.nih.gov/32214244/}{PubMed})
"TCGA.contaminants"