prepData {CATALYST} | R Documentation |
Data preparation
prepData( x, panel, md, features = 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")) )
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:
|
features |
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 |
data(PBMC_fs, PBMC_panel, PBMC_md) prepData(PBMC_fs, PBMC_panel, PBMC_md)