getOverallTrajectory-CombinedDataSet-method: get Overall Trajectory

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

get Overall Trajectory

Description

This function infers the overall trajectory structure from CombinedDataSet using .

Usage

## S4 method for signature 'CombinedDataSet'
getOverallTrajectory(
  CombinedDataSet,
  reducedDim = "UMAP",
  start.clus = NULL,
  end.clus = NULL,
  dist.method = "slingshot",
  use.median = FALSE,
  ...
)

Arguments

reducedDim	The dimensionality reduction to be used. Can be a matrix or a character identifying which element of reducedDim(data) is to be used. If multiple dimensionality reductions are present and this argument is not provided, the first element will be used by default.
start.clus	(optional) character, indicates the starting cluster(s) from which lineages will be drawn.
end.clus	(optional) character, indicates which cluster(s) will be forced to be leaf nodes in the graph.
dist.method	(optional) character, specifies the method for calculating distances between clusters. Default is "slingshot", see createClusterMST for details.
use.median	logical, whether to use the median (instead of mean) when calculating cluster centroid coordinates. Default is 'TRUE'.
data	A class of CombinedDataSet object

Details

Given a CombinedDataSet object, this function infers the overall cell trajectory using the . To reduce noise, clones with less than 5 cells are removed before trajectory inference.

Value

A class of TrajectoryDataSet object

Examples

TCR <-read.csv('/PATH/TO/YOUR/scTCR-seqData/',header=T)
load('Mice.sub.rda')
Combined <- getCombinedDataSet(TCR,Mice.sub)
Trajectory <- getOverallTrajectory(Combined,reducedDim = NULL,start.clus = NULL, end.clus = NULL, dist.method = 'slingshot', use.median = TRUE)

JuanXie19/LRT documentation built on April 14, 2025, 7:09 p.m.