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:

  - `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

### 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]