clonoStats-class | R Documentation |
clonoStats
object classThe 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.
## 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)
object |
a |
An object of class clonoStats
.
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
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).
clonoStats
data('contigs')
cs <- clonoStats(contigs)
cs
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