R/HelperFuntions.r

In JuanXie19/LRT: LRT (Lineage estimation by integrative analysis of single-cell RNA-seq and TCR-seq data)

#' @rdname seuratClusterLabels
#' @import Seurat
#' @export
setMethod(
	f ='seuratClusterLabels',
	signature = 'CombinedDataSet',
	definition = function(CombinedDataSet) CombinedDataSet@seurat$clusters
)

#' @rdname getTCRs
#' @import Seurat
#' @export
setMethod(
	f = 'getTCRs',
	signature = 'CombinedDataSet',
	definition = function(CombinedDataSet) CombinedDataSet@seurat$CTaa
)

#' @rdname lrtLineages
#' @import slingshot
#' @import TrajectoryUtils
#' @export
setMethod(
	f = 'lrtLineages',
	signature = 'TrajectoryDataSet',
	definition = function(TrajectoryDataSet) TrajectoryDataSet@slingLineages
)

#' @rdname lrtParams
#' @import slingshot
#' @import TrajectoryUtils
#' @export
setMethod(
	f = 'lrtParams',
	signature = 'TrajectoryDataSet',
	definition = function(TrajectoryDataSet) TrajectoryDataSet@trajectoryParams
)