daFrame-class {CATALYST} | R Documentation |
Represents the data returned by and used throughout differential analysis.
assays
list of length one containing the arcsinh-transformed expressions.
rowData
the metadata information for each event, and its cluster ID
as inferred by the initial FlowSOM
clustering.
colData
a data.frame with the following columns:
marker_name
original column name in the input flowSet
marker_class
one of "type"
or "state"
metadata
a named list containing:
design
: the original metadata-table
panel
: the original panel-table
n_cells
: the number of events measured per sample
SOM_codes
: a k x p matrix of SOM codes, where
k = no. of clusters, and p = no. of measurement parameters
cluster_codes
: cluster codes for the initial FlowSOM
clustering, the ConsensusClusterPlus metaclustering, and manual
mergings done with mergeClusters
daFrame(x, panel, md, cols_to_use = NULL, cofactor = 5, panel_cols = list(channel = "fcs_colname", antigen = "antigen"), md_cols = list(file = "file_name", id = "sample_id", factors = c("condition", "patient_id")))
x |
a |
panel |
a 2 column |
md |
a
|
cols_to_use |
a logical vector OR numeric vector of indices OR character vector
of column names. Specifies which columns to keep from the input
|
cofactor |
numeric. Cofactor to use for arcsinh-transformation. |
panel_cols |
a named list specifying column names of |
md_cols |
a named list specifying column names of |
an object of class SummarizedExperiment
.
Helena Lucia Crowell crowellh@student.ethz.ch