RepSeqExperiment-class: Class RepSeqExperiment

In ph-pham/RepSeq: Analysis of High-throughput sequencing repertoire data (RepSeqTools)

Description

An S4 class to represent a Hight Throuput Sequencing Immune Repertoire Experiment.

[ Extract parts of RepSeqExperiment.

Usage

assay(object)

assay(object, i, j) <- value

mData(object)

mData(object) <- value

sData(object)

sData(object) <- value

History(object)

History(object) <- value

## S4 method for signature 'RepSeqExperiment'
assay(object)

## S4 replacement method for signature 'RepSeqExperiment'
assay(object, i, j) <- value

## S4 method for signature 'RepSeqExperiment'
mData(object)

## S4 replacement method for signature 'RepSeqExperiment'
mData(object) <- value

## S4 method for signature 'RepSeqExperiment'
sData(object)

## S4 replacement method for signature 'RepSeqExperiment'
sData(object) <- value

## S4 method for signature 'RepSeqExperiment'
History(object)

## S4 replacement method for signature 'RepSeqExperiment'
History(object) <- value

## S4 method for signature 'RepSeqExperiment'
show(object)

## S4 method for signature 'RepSeqExperiment'
names(x)

## S4 replacement method for signature 'RepSeqExperiment'
names(x) <- value

## S4 method for signature 'RepSeqExperiment,ANY,ANY,ANY'
x[i, j, drop]

is.RepSeqExperiment(x)

Arguments

object	a RepSeqExperiment object
i	indice(s) of clonotype(s) to extract
j	indice(s) of sample(s) to extract
value	either numeric, character or data frame
x	an object
drop	If TRUE the result is coerced to the lowest possible dimension

Value

an object of class [RepSeqExperiment]

Slots

assayData

a data.table containing information about clonotype.

sampleData

a data frame containing sample information such as treatment groups, species, ...

metaData

a list of meta data

History

a data frame registering operations done on the object.

Author(s)

H. P. Pham (mailto: hp.pham(a)pareanbiotech.fr, #chokomlabreizh)

ph-pham/RepSeq documentation built on Dec. 22, 2021, 7:47 a.m.