Startrac | R Documentation |
The Startrac object store the data for tcr-based T cell dynamics analyis. The slots contained in Startrac object are listed below:
aid
character. aid of the object, used for identification of the object. For example, patient id. default: "AID"
cell.data
data.frame. Each line for a cell, and these columns as required: 'Cell_Name', 'clone.id', 'patient', 'majorCluster', 'loc'
cell.perm.data
object. list of 'Startrac“ objects constructed from permutated cell data
clonotype.data
data.frame. Each line for a clonotype; contain the clonotype level indexes information
cluster.data
data.frame. Each line for a cluster; contain the cluster level indexes information
pIndex.migr
data.frame. Each line for a cluster; pairwise migration index between the two locations indicated in the column name.
pIndex.tran
data.frame. Each line for a cluster; pairwise transition index betwwen the two major clusters indicated by the row name and column name.
cluster.sig.data
data.frame. Each line for a cluster; contains the p values of cluster indices.
pIndex.sig.migr
data.frame. Each line for a cluster; contains the p values of pairwise migration indices.
pIndex.sig.tran
data.frame. Each line for a cluster; contains the p values of pairwise transition indices.
clonotype.dist.loc
matrix. Each line for a clonotype and describe the cells distribution among the locations.
clonotype.dist.cluster
matrix. Each line for a clonotype and describe the cells distribution among the clusters.
clust.size
array. Number of cells of each major cluster.
patient.size
array. Number of cells of each patient.
clone.size
array. Number of cells of each clone.
clone2patient
array. Mapping from patient id to clone id.
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