R: Differential analysis frame class

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]