R/data.R

In rliger: Linked Inference of Genomic Experimental Relationships

#' liger object of PBMC subsample data with Control and Stimulated datasets
#' @format \linkS4class{liger} object with two datasets named by "ctrl" and
#' "stim".
#' @source https://www.nature.com/articles/nbt.4042
#' @references Hyun Min Kang and et. al., Nature Biotechnology, 2018
"pbmc"

#' liger object of PBMC subsample data with plotting information available
#' @description This data was generated from data \code{"pbmc"} with default
#' parameter integration pipeline: normalize, selectGenes, scaleNotCenter,
#' runINMF, runCluster, runUMAP. To minimize the object size distributed with
#' the package, rawData and scaleData were removed. Genes are downsampled to
#' the top 50 variable genes, for smaller normData and \eqn{W} matrix.
#' @format \linkS4class{liger} object with two datasets named by "ctrl" and
#' "stim".
#' @source https://www.nature.com/articles/nbt.4042
#' @references Hyun Min Kang and et. al., Nature Biotechnology, 2018
"pbmcPlot"

#' liger object of bone marrow subsample data with RNA and ATAC modality
#' @format \linkS4class{liger} object with two dataset named by "rna" and "atac"
#' @source https://www.nature.com/articles/s41587-019-0332-7
#' @references Jeffrey M. Granja and et. al., Nature Biotechnology, 2019
"bmmc"