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:

metadata

a named list containing:

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]