Startrac {scRepertoire} | R Documentation

## 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.

[Package scRepertoire version 1.2.0 Index]