daFrame-class {CATALYST}R Documentation

Differential analysis frame class

Description

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:

Usage

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, ...)

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)

...

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 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

an object of class daFrame.

Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

Examples

data(PBMC_fs, PBMC_panel, PBMC_md)
daFrame(PBMC_fs, PBMC_panel, PBMC_md)


[Package CATALYST version 1.8.7 Index]