cfList-class {cytofast} | R Documentation

## Class cfList

### Description

This is an S4 class that contains all the data and results for the cytofast workflow. Most functions in this package will both use and return a `cfList`.

### Details

This class is used througout the cytofast workflow, most functions in this package will both use and return a `cfList`. FCS files created by Cytosplore can be easily read in with `readCytosploreFCS`) and will be returned as a cfList. It is also possible to manually create instances of this class if another clustering method is preferred. Below an example is shown for `FlowSOM`.

### Slots

`samples`

  data frame containing all meta information on each sample

`expr`

  data frame containing the marker expression

`counts`

  data frame containing (standardized) cell counts per cluster and per sample

`results`

  list containing any results

### Methods

`samples`

  a method for obtaining the samples data

`expr`

  a method for obtaining the marker expression

`counts`

  a method for obtaining the cell counts

`results`

  a method for obtaining any results from performed tests

### Examples

    ### manually create instance of cfList class
    library(FlowSOM)

    ## Cluster with FlowSOM
    dirFCS <- system.file("extdata", package="cytofast")
    fSOM <- FlowSOM(input = dirFCS,
                    transform = FALSE,
                    scale = FALSE,
                    colsToUse = c(9:11, 15:52),
                    nClus = 10, # Note that this is an ambiguous choice
                    seed = 123)

    ## expr slot
    # retrieve clusters
    clusterID <- as.factor(fSOM$FlowSOM$map$mapping[,1])
    levels(clusterID) <- fSOM$metaclustering

    # retrieve samples (As example, we assume each FCS file is its own sample)
    sampleID <- lapply(fSOM$FlowSOM$metaData, function(x){rep(x[1], each = length(x[1]:x[2]))})
    attr(sampleID, 'names') <- NULL
    sampleID <- as.factor(unlist(sampleID))
    levels(sampleID) <- paste("ID", 1:10, sep="_")

    exprD <- data.frame(clusterID,
                        sampleID,
                        fSOM$FlowSOM$data[, c(9:11, 15:52)])

    ## samples slot
    samplesD <- data.frame(sampleID = levels(sampleID),
                           group = rep(c("group1", "group1"), each=5))

    ## create cfList
    cfList(samples = samplesD,
           expr = exprD)

[Package cytofast version 1.4.0 Index]