R/data.R

In adw96/DivNet: Diversity Estimation in Networked Ecological Communities

#' phyloseq object from Lee et al (2015)
#'
#' A dataset containing the abundance table, covariate information, and taxonomy of a 16S study of basalts on the Dorado Outcrop
#'
#' @format A phyloseq object containing the data from Lee et al (2015)
#'
#'
#' @source \url{https://astrobiomike.github.io/amplicon/workflow_ex}
#' @references "Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades" by Lee et. al (2015), Frontiers in Microbiology
"Lee"


#' OTU data from Sinha et al. (2017)
#'
#' A dataset containing OTU counts reported by Sinha et al. (2017)
#'  in colorectal cancer patients and controls
#' as sequenced by sequencing laboratory B and processed by bioinformatics
#' laboratory 2.
#'
#' @format A dataframe containing a subset of data from Sinha et al. (2017)
#'
#'
#' @source \url{https://www.nature.com/articles/nbt.3981}
#' @references "Sinha, Rashmi, et al. "Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium." Nature biotechnology 35.11 (2017): 1077-1086.
"B2"


#' Species data from Sinha et al. (2017) in phyloseq format
#'
#' A dataset containing OTU counts reported by Sinha et al. (2017)
#'  in colorectal cancer patients and controls
#' as sequenced by sequencing laboratory B and processed by bioinformatics
#' laboratory 2.
#'
#' @format A phyloseq object containing a subset of data from Sinha et al. (2017)
#'
#'
#' @source \url{https://www.nature.com/articles/nbt.3981}
#' @references "Sinha, Rashmi, et al. "Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium." Nature biotechnology 35.11 (2017): 1077-1086.
"B2_phyloseq"