StartracDiversity {scRepertoire}R Documentation

Diversity indices for single-cell RNA-seq

Description

This function utilizes the Startrac R package derived from [PMID: 30479382](https://pubmed.ncbi.nlm.nih.gov/30479382/) Required to run the function, the "type" variable needs to include the difference in where the cells were derived. The output of this function will produce 3 indices: expa (clonal expansion), migra (cross-tissue migration), and trans (state transition). In order to understand the underlying analyses of the outputs please read and cite the linked manuscript.

Usage

StartracDiversity(
  sc,
  type = "Type",
  sample = NULL,
  by = "overall",
  exportTable = FALSE
)

Arguments

sc

The seurat or SCE object to visualize after combineExpression(). For SCE objects, the cluster variable must be in the meta data under "cluster".

type

The column header in the meta data that gives the where the cells were derived from, not the patient sample IDs

sample

The column header corresponding to individual samples or patients.

by

Method to subset the indices by either overall (across all samples) or by specific group

exportTable

Returns the data frame used for forming the graph

Value

ggplot object of Startrac diversity metrics

Examples

 
#Getting the combined contigs
combined <- combineTCR(contig_list, rep(c("PX", "PY", "PZ"), each=2), 
rep(c("P", "T"), 3), cells ="T-AB")

#Getting a sample of a Seurat object
screp_example <- get(data("screp_example"))
screp_example <- combineExpression(combined, screp_example)

#Using occupiedscRepertoire()
StartracDiversity(screp_example, type = "Type", sample = "Patient", by = "overall")



[Package scRepertoire version 1.3.1 Index]