prepData {CATALYST}R Documentation

Data preparation

Description

Data preparation

Usage

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"))
)

Arguments

x

a flowSet holding all samples or a path to a set of FCS files.

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:

  • file_name: the FCS file name

  • sample_id: a unique sample identifier

  • patient_id: the patient ID

  • condition: brief sample description (e.g. reference/stimulated, healthy/diseased)

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 panel that contain the channel names, targeted protein markers, and (optionally) marker classes.

md_cols

a named list specifying the column names of md that contain the FCS file names, sample IDs, and factors of interest (batch, condition, treatment etc.).

Value

a SingleCellExperiment.

Examples

data(PBMC_fs, PBMC_panel, PBMC_md)
prepData(PBMC_fs, PBMC_panel, PBMC_md)


[Package CATALYST version 1.10.3 Index]