AbSeqCRep-class {abseqR} | R Documentation

## S4 class - AbSeqCompositeRepertoire analysis object

### Description

AbSeqCRep is a collection of AbSeqRep S4 objects. This S4 class contains multiple samples(repertoires) and it can be "combined" with other samples by using the `+` operator to create an extended AbSeqCRep object. This value, in turn, can be used as the first argument to report which generates a comparison between all samples included in the `+` operation.

Users do not manually construct this class, but rather indirectly obtain this class object as a return value from the `+` operation between two AbSeqRep objects, which are in turn, obtained indirectly from abseqReport and report functions. It is also possible to obtain this class object by `+` (adding) AbSeqCRep objects.

### Value

AbSeqCRep

### Slots

`repertoires`

  list of AbSeqRep objects.

### See Also

AbSeqRep

### Examples

    # Use example data from abseqR as abseqPy's output, substitute this
    # with your own abseqPy output directory
    abseqPyOutput <- tempdir()
    file.copy(system.file("extdata", "ex", package = "abseqR"), abseqPyOutput, recursive=TRUE)
    samples <- abseqReport(file.path(abseqPyOutput, "ex"), report = 0)

    # The provided example data has PCR1, PCR2, and PCR3 samples contained within
    # pcr12 and pcr13 are instances of AbSeqCRep
    pcr12 <- samples[["PCR1"]] + samples[["PCR2"]]
    pcr13 <- samples[["PCR1"]] + samples[["PCR3"]]

    # all_S is also an instance of AbSeqCRep
    all_S <- pcr12 + pcr13

[Package abseqR version 1.12.0 Index]