daFrame-class {CATALYST} | R Documentation |
Represents the data returned by and used throughout differential analysis.
assays
a list of length 1 containing the measurement data.
rowData
an object of the DataFrame-class
containing the row metadata.
colData
an object of the DataFrame-class
containing the column metadata.
metadata
a named list containing:
experimental_design
: the original metadata table.
n_cells
: number of events (cells) measured per sample.
cofactor
: numeric cofactor used for arcsinh-transformation.
cluster_codes
:
cluster codes for the initial FlowSOM clustering ("som100"
),
the ConsensusClusterPlus metaclustering ("metaX"
), and all
manual mergings done with mergeClusters
.
delta_area
: the Delta Area plot
(see ConsensusClusterPlus for details).
experimental_design
: the original metadata table
daFrame(x, panel, md, ...) ## S4 method for signature 'flowSet,data.frame,data.frame' daFrame(x, panel, md, cols_to_use = NULL, cofactor = 5, panel_cols = list(channel = "fcs_colname", antigen = "antigen", class = "marker_class"), md_cols = list(file = "file_name", id = "sample_id", factors = c("condition", "patient_id"))) ## S4 method for signature 'character,data.frame,data.frame' daFrame(x, panel, md, ...) ## S4 method for signature 'daFrame,matrix,ANY' daFrame(x, panel, md, ...) ## S4 method for signature 'daFrame,ANY,matrix' daFrame(x, panel, md, ...)
x |
a |
panel |
a data.frame containing, for each channel, its column name in the input data, targeted protein marker, and (optionally) class ("type", "state", or "none"). |
md |
a table with column describing the experiment. An exemplary metadata table could look as follows:
|
... |
optional arguments. |
cols_to_use |
a logical vector, numeric vector of column indices, or character vector of channel names. Specified which column to keep from the input data. Defaults to the channels listed in the input panel. |
cofactor |
numeric cofactor to use for arcsinh-transformation. |
panel_cols |
a names list specifying the column names of |
md_cols |
a named list specifying the column names of |
an object of class daFrame
.
Helena Lucia Crowell helena.crowell@uzh.ch
data(PBMC_fs, PBMC_panel, PBMC_md) daFrame(PBMC_fs, PBMC_panel, PBMC_md)