R/example.seasnake.R

In BIGslu/kimma: Kinship In Mixed Model Analysis of RNA-seq

#' Example SEAsnake outputs
#'
#' @format Class 'list' with 5 slots:
#' \enumerate{
#' \item \strong{fcounts} A data frame with 19118 rows and 13 columns
#' \describe{
#'   \item{Geneid}{character. ENSEMBL gene ID.}
#'   \item{lib1}{numeric. Counts in library 1.}
#'   \item{lib2}{numeric. Counts in library 2.}
#'   \item{lib3}{numeric. Counts in library 3.}
#'   \item{lib4}{numeric. Counts in library 4.}
#'   \item{lib5}{numeric. Counts in library 5.}
#'   \item{lib6}{numeric. Counts in library 6.}
#'   \item{lib7}{numeric. Counts in library 7.}
#'   \item{lib8}{numeric. Counts in library 8.}
#'   \item{lib9}{numeric. Counts in library 9.}
#'   \item{lib10}{numeric. Counts in library 10.}
#'   \item{lib11}{numeric. Counts in library 11.}
#'   \item{lib12}{numeric. Counts in library 12.}
#'       }
#'
#' \item \strong{flagstat} A data frame with 12 rows and 17 columns
#' \describe{
#'   See http://www.htslib.org/doc/samtools-flagstat.html
#'       }
#'
#' \item \strong{picard} A data frame with 12 rows and 31 columns
#' \describe{
#'   See http://broadinstitute.github.io/picard/picard-metric-definitions.html#RnaSeqMetrics
#'   }
#'
#' \item \strong{patient} A data frame with 5 rows and 4 columns
#' \describe{
#'   \item{ptID}{character. patient ID.}
#'   \item{asthma}{character. Patient classification as healthy or asthma.}
#'   \item{age}{numeric. Patient age in years.}
#'   \item{sex}{character. Patient biological sex: male or female.}
#'   }
#'
#' \item \strong{sample} A data frame with 12 rows and 4 columns
#' \describe{
#'   \item{libID}{character. Libray ID.}
#'   \item{ptID}{character. Patient ID.}
#'   \item{virus}{character. Sample treatment: media control (none) or human rhinovirus infected (HRV).}
#'   \item{batch}{character. Sequenceing batch: A or B.}
#'   }
#'   }
#'
#' @source \url{https://github.com/BIGslu/SEAsnake}
#' @references Dill-McFarland et al. 2022 Eosinophil-mediated suppression and Anti-IL-5 enhancement of plasmacytoid dendritic cell interferon responses in asthma. J Allergy Clin Immunol. 150(3):666-675. doi: 10.1016/j.jaci.2022.03.025
#' @description A list contains SEAsnake results including gene counts, library quality metrics, and sample metadata.
#' @docType data
#' @name example.seasnake
#' @keywords datasets
"example.seasnake"