The Startrac Class

Description

The Startrac object store the data for tcr-based T cell dynamics analyis. The slots contained in Startrac object are listed below:

Slots

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.