clonoStats-class: 'clonoStats' object class

In kstreet13/VDJdive: Analysis Tools for 10X V(D)J Data

clonoStats object class

Description

The clonoStats class is designed to hold the output of the clonoStats function. This always includes two group-level summaries: clonotype abundances and clonotype frequencies. "Group" most often refers to sample of origin, but may alternatively refer to any partitioning of cells, such as clusters. Clonotype names are stored efficiently in two factors. Additionally, a large, sparse matrix of each cell's clonotype assignment may be included.

Usage

## S4 method for signature 'clonoStats'
show(object)

clonoNames(object)

## S4 method for signature 'clonoStats'
clonoNames(object)

## S4 method for signature 'SingleCellExperiment'
clonoNames(object)

clonoAbundance(object)

## S4 method for signature 'clonoStats'
clonoAbundance(object)

## S4 method for signature 'SingleCellExperiment'
clonoAbundance(object)

clonoFrequency(object)

## S4 method for signature 'clonoStats'
clonoFrequency(object)

## S4 method for signature 'SingleCellExperiment'
clonoFrequency(object)

clonoAssignment(object)

## S4 method for signature 'clonoStats'
clonoAssignment(object)

## S4 method for signature 'SingleCellExperiment'
clonoAssignment(object)

clonoGroup(object)

## S4 method for signature 'clonoStats'
clonoGroup(object)

## S4 method for signature 'SingleCellExperiment'
clonoGroup(object)

Arguments

object

a clonoStats object or SingleCellExperiment object containing clonoStats results.

Value

An object of class clonoStats.

Functions

• show(clonoStats): a short summary of a clonoStats object.

• clonoNames(): Get the full clonotype names

• clonoAbundance(): Get the clonotype abundance matrix (clonotype counts per group).

• clonoFrequency(): Get the matrix of clonotype frequencies (singletons, doubletons, etc. per group).

• clonoAssignment(): Get the matrix of cell-level clonotype assignments (mapping cells to clonotypes).

• clonoGroup(): Get the factor variable of group labels

Slots

abundance

Summary table of clonotype abundances within each group (sample). Provides specific information about how often each clonotype is observed in each group.

frequency

Summary table of clonotype frequencies within each group (sample). Provides a summary of clonotype abundances (ie. number of singletons, doubletons, etc.).

group

Factor variable giving the group of origin for each cell.

assignment

Optional matrix of clonotype assignments in each individual cell. Rows correspond to cells and row sums are all 0 or 1. When using clonoStats with method = "unique" or method = "CellRanger", all values will be 0 or 1. With method = "EM", fractional values are allowed, representing the assignment confidence.

names1

Factor listing the first component of each clonotype name (alpha chains, for TCR data).

names2

Factor listing the second component of each clonotype name (beta chains, for TCR data).

See Also

clonoStats

Examples

data('contigs')
cs <- clonoStats(contigs)
cs

kstreet13/VDJdive documentation built on May 31, 2024, 1:26 p.m.