AbSeqCRep-class: S4 class - AbSeqCompositeRepertoire analysis object

In abseqR: Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

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

abseqR documentation built on Nov. 8, 2020, 8:28 p.m.