getClonotypeLineages: Infer clonotype lineage structure from 'CombinedDatSet'

In JuanXie19/TCRlineageClust:

Description

This function infers the clonotype lineages structure from CombinedDataSet.

Usage

getClonotypeLineages(CombinedDataSet, ...)

## S4 method for signature 'CombinedDataSet'
getClonotypeLineages(
  CombinedDataSet,
  start.clus = NULL,
  end.clus = NULL,
  dist.method = "simple",
  use.median = TRUE,
  ...
)

Arguments

CombinedDataSet	The CombinedDataSet object obtained from getCombinedDataSet
...	Additional arguments to specify how lineages are constructed from clusters.
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 "simple", 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 constructs the minimum spanning tree(s) on cells sharing the same clonotype. These cells may belong to different clusters defined by scRNA-seq features, therefore a graph can be constructed with node being the center of a cluster, and weight of an edge being the distance between the nodes. MST is built based on such a graph.

Once the MST is known, lineages are identified in any tree with at least two clusters. For a given tree, if there is an annotated starting cluster, every possible path out of a starting cluster and ending in a leaf that isn't another starting cluster will be returned. If no starting cluster is annotated, one will be chosen by a heuristic method, but this is not recommended.

Value

A class of TrajectoryDataSet object

Examples

TCR <-read.csv('C:/TCR-seq/Gang/GSE158896_RAW/combinedTCR_2cells.csv',header=T)
load('Mice.sub.rda')
Combined <- getCombinedDataSet(TCR,Mice.sub)
Trajectory <- getClonotypeLineages(Combined,start.clus = NULL, end.clus = NULL, dist.method = 'simple', use.median = TRUE)

JuanXie19/TCRlineageClust documentation built on Feb. 26, 2022, 12:33 a.m.