daFrame-class {CATALYST} | R Documentation

## Differential analysis frame class

### Description

Represents the data returned by and used throughout differential analysis.

`assays`

  list of length one containing the arcsinh-transformed expressions.

`rowData`

  the metadata information for each event, and its cluster ID as inferred by the initial `FlowSOM` clustering.

`colData`

  a data.frame with the following columns:

  - `marker_name` original column name in the input `flowSet`

  - `marker_class` one of `"type"` or `"state"`

`metadata`

  a named list containing:

  - `design`: the original metadata-table

  - `panel`: the original panel-table

  - `n_cells`: the number of events measured per sample

  - `SOM_codes`: a k x p matrix of SOM codes, where k = no. of clusters, and p = no. of measurement parameters

  - `cluster_codes`: cluster codes for the initial FlowSOM clustering, the ConsensusClusterPlus metaclustering, and manual mergings done with `mergeClusters`

### Usage

    daFrame(x, panel, md, cols_to_use = NULL, cofactor = 5,
      panel_cols = list(channel = "fcs_colname", antigen = "antigen"),
      md_cols = list(file = "file_name", id = "sample_id", factors =
      c("condition", "patient_id")))

### Arguments

`x` | a `flowSet` holding all samples OR a character vector that specifies a path to set of FCS files.
`panel` | a 2 column `data.frame` that contains for each marker of interest i) its column name in the FCS file, and ii) the targeted protein marker.
`md` | a `data.frame` with columns describing the experiment. An exemplary metadata table could look as follows: `file_name`: the FCS file name `sample_id`: a unique sample identifier `condition`: brief sample description (e.g. REF) `patient_id`: the patient ID
`cols_to_use` | a logical vector OR numeric vector of indices OR character vector of column names. Specifies which columns to keep from the input `flowSet`/FCS files.
`cofactor` | numeric. Cofactor to use for arcsinh-transformation.
`panel_cols` | a named list specifying column names of `panel` that contain i) the original channel names in `fs`, and ii) the targeted protein marker. Elements must be named `"channel"` and `"antigen"`.
`md_cols` | a named list specifying column names of `md` that contain i) the FCS file names, ii) unique sample identifiers, and iii) a character vector of factors descriptive of the samples (e.g. condition, treatment, ect.). Elements must be named `"file"`, `"id"`, and `"factors"`.

### Value

an object of class `SummarizedExperiment`.

### Author(s)

Helena Lucia Crowell crowellh@student.ethz.ch

[Package CATALYST version 1.4.2 Index]