R/data.R

In peco: A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

#' @title Training data from 888 single-cell samples and 101 top cyclic genes
#'
#' @description Pre-computed results. Applied \emph{fit_cyclic_many} to 888
#'   single-cell samples that have both normalized gene expression values and
#'   cell cycle labels to obtain training results that can be used as input
#'   for predicting cell cycle phase in other data.
#'
#' @format A list with the follwing elements
#'
#' \describe{
#'   \item{predict.yy}{Estimated cyclic expression values in the training data}
#'   \item{cellcycle_peco_ordered}{Training labels ordered from 0 to 2pi}
#'   \item{cell_cycle function}{Nonparametric function of cyclic gene expression
#'   trend obtained by trendfilter function in genlasso}
#'   \item{pve}{Proportion of variance explained in each gene by the
#'   cell cycl phase label}
#'  }
#'
#' @docType data
#'
#' @usage data(training_human)
#'
#' @keywords data
"training_human"

#' Molecule counts of the 101 significant cyclical genes in the 888 samples
#' analyzed in the study.
#'
#' A SingleCellExperiment object (require SingleCellExperiment package)
#' including molecule count data after gene and smaple filtering.
#' The `colData()` slot contains sample phenotype information and
#' the `rowData()` slot contains gene feature information.
#'
#' @format A SingleCellExperiment object with 888 samples and the 101
#'     significant cyclic genes,
#' \describe{
#'     \item{theta}{Inferred angles of each cell along
#'         a circle, also known as FUCCI phase.}
#' }
#'
#' @docType data
#'
#' @usage data(sce_top101genes)
#'
#' @keywords data
"sce_top101genes"

#' @title Traing model results among samples from 5 individuals.
#'
#' @description Pre-computed results. Applied \emph{cycle_npreg_insample} to
#'   obtain gene-specific cyclic trend parameters using samples from 5
#'   individuals
#'
#' @format A list with the follwing elements
#' \describe{
#'   \item{Y}{a data.frame (gene by sample) of quantile-normailzed gene
#'   expression values}
#'   \item{theta}{a vector of cell cycl phase values (range between 0 to 2pi)}
#'   \item{sigma_est}{a vector of estimated standard errors}
#'   \item{funs_est}{a list of estimated cyclic functions}
#' }
#'
#' @docType data
#'
#' @usage data(model_5genes_train)
#'
#' @keywords data
"model_5genes_train"

#' @title A SingleCellExperiment object
#'
#' @description Pre-computed results. Applied \emph{cycle_npreg_outsample} and
#'   results stored in \emph{model_5genes_train} to predict cell cycle phase for
#'   single-cell samples of NA19098. The predicted cell cycle is stored as
#'   variable \emph{cellcycle_peco}.
#'
#' @format A list with the follwing elements
#'
#' \describe{
#'   \item{cellcycle_peco}{Predict cell cycle,
#'    the values ranged between 0 to 2pi}
#'  }
#'
#' @docType data
#'
#' @usage data(model_5genes_predict)
#'
#' @keywords data
"model_5genes_predict"



#' @title list of cell cycle genes identified in Whitfield et al. 2002.
#'
#' @description List of cell cycle genes and their associated cell cycle state as
#'   reported in Whitfield et al. 2002.
#'
#' @format A list with the follwing elements
#'
#' \describe{
#'   \item{hgnc}{Gene symbol}
#'   \item{ensembl}{ENSEMBL gene ID}
#'   \item{phase}{Marker phase identified in Whitfield et al. 2002}
#'  }
#'
#' @docType data
#'
#' @usage data(cellcyclegenes_whitfield2002)
#'
#' @keywords data
"cellcyclegenes_whitfield2002"