dbFrame-methods {CATALYST} | R Documentation

## Extraction and replacement methods for objects of class `dbFrame`

### Description

Methods for replacing and accessing slots in a `dbFrame`.

### Usage

    bc_key(x)

    bc_ids(x)

    deltas(x)

    normed_bcs(x)

    mhl_dists(x)

    sep_cutoffs(x)

    mhl_cutoff(x)

    counts(x)

    yields(x)

    ## S4 method for signature 'dbFrame'
    exprs(object)

    ## S4 method for signature 'dbFrame'
    bc_key(x)

    ## S4 method for signature 'dbFrame'
    bc_ids(x)

    ## S4 method for signature 'dbFrame'
    deltas(x)

    ## S4 method for signature 'dbFrame'
    normed_bcs(x)

    ## S4 method for signature 'dbFrame'
    mhl_dists(x)

    ## S4 method for signature 'dbFrame'
    sep_cutoffs(x)

    ## S4 method for signature 'dbFrame'
    mhl_cutoff(x)

    ## S4 method for signature 'dbFrame'
    counts(x)

    ## S4 method for signature 'dbFrame'
    yields(x)

    ## S4 replacement method for signature 'dbFrame,numeric'
    mhl_cutoff(x) <- value

    ## S4 replacement method for signature 'dbFrame,ANY'
    mhl_cutoff(x) <- value

    ## S4 replacement method for signature 'dbFrame,numeric'
    sep_cutoffs(x) <- value

    ## S4 replacement method for signature 'dbFrame,ANY'
    sep_cutoffs(x) <- value

### Arguments

`x, object` | a `dbFrame`.
`value` | the replacement value.

### Value

`exprs`

  extracts the raw data intensities.

`bc_key`

  extracts the barcoding scheme.

`bc_ids`

  extracts currently made event assignments.

`deltas`

  extracts barcode separations computed from normalized intensities. `sep_cutoffs` apply to these values (see `applyCutoffs`).

`normed_bcs`

  extracts normalized barcode intensities (see `assignPrelim`).

`sep_cutoffs`, `sep_cutoffs<-`

  extracts or replaces separation cutoffs. If option `sep_cutoffs` is not specified, these will be used by `applyCutoffs`. Replacement value must be a non- negative numeric with length one or same length as the number of barcodes.

`mhl_cutoff`, `mhl_cutoff<-`

  extracts or replaces the Mahalanobis distance threshold above which events are to be unassigned. Replacement value must be a single non-negative and non-zero numeric.

`counts`

  extract the counts matrix (see `dbFrame`).

`yields`

  extract the yields matrix (see `dbFrame`).

### Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

### Examples

    data(sample_ff, sample_key)
    re <- assignPrelim(x = sample_ff, y = sample_key)

    # set global cutoff parameter
    sep_cutoffs(re) <- 0.4
    re <- applyCutoffs(x = re)

    # subset a specific population, e.g. A1: 111000
    a1 <- bc_ids(re) == "A1"
    head(exprs(sample_ff[a1, ]))

    # subset unassigned events
    unassigned <- bc_ids(re) == 0
    head(exprs(sample_ff[unassigned, ]))

[Package CATALYST version 1.10.3 Index]