ei {CATALYST}R Documentation

Extraction and replacement methods for objects of class daFrame

Description

Methods for accessing slots in a daFrame.

Usage

ei(x)

n_cells(x)

marker_classes(x)

type_markers(x)

state_markers(x)

sample_ids(x)

cluster_codes(x)

cluster_ids(x, ...)

## S4 method for signature 'daFrame'
reducedDimNames(x)

## S4 method for signature 'daFrame'
reducedDims(x)

## S4 method for signature 'daFrame'
reducedDim(x, dr = 1)

## S4 replacement method for signature 'daFrame,character'
reducedDimNames(x) <- value

## S4 method for signature 'daFrame'
exprs(object)

## S4 method for signature 'daFrame'
ei(x)

## S4 method for signature 'daFrame'
n_cells(x)

## S4 method for signature 'daFrame'
marker_classes(x)

## S4 method for signature 'daFrame'
type_markers(x)

## S4 method for signature 'daFrame'
state_markers(x)

## S4 method for signature 'daFrame'
sample_ids(x)

## S4 method for signature 'daFrame'
cluster_codes(x)

## S4 method for signature 'daFrame'
cluster_ids(x, k = NULL)

## S4 method for signature 'daFrame,ANY,ANY,ANY'
x[i, j]

Arguments

x, object

a daFrame.

...

optional arguments.

dr

character string specifying the dim. reduction to extract.

value

a character vector containing the desired dimensionality reduction names.

k

character string specifying the clustering to extract. Valid values are names(cluster_codes(x)).

i, j

indices specifying elements to extract.

Value

exprs

extracts the arcsinh-transformed expressions.

n_cells

extracts the number of events measured per sample.

type_markers

extracts the antigens used for clustering.

state_markers

extracts antigens that were not used for clustering.

sample_ids

extracts the sample IDs as specified in the metadata-table.

cluster_codes

extracts a data.frame containing cluster codes for the FlowSOM clustering, the ConsensusClusterPlus metaclustering, and all mergings done through mergeClusters.

cluster_ids

extracts the numeric vector of cluster IDs as inferred by FlowSOM.

Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

Examples

# construct daFrame
data(PBMC_fs, PBMC_panel, PBMC_md)
re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)

# run clustering
re <- cluster(re)

# view data summary
library(SummarizedExperiment)
cbind(metadata(re)$experiment_info, cells=n_cells(re))

# access row / cell data
head(rowData(re))
plot(table(cluster_ids(re)))

# access marker information
type_markers(re)
state_markers(re)

# get cluster ID correspondece between 2 clusterings
old_ids <- seq_len(20)
m <- match(old_ids, cluster_codes(re)$`meta20`)
new_ids <- cluster_codes(re)$`meta12`[m]
data.frame(old_ids, new_ids)

# plot relative change in area under CDF curve vs. k
metadata(re)$delta_area

[Package CATALYST version 1.8.7 Index]