sub-sub-ContigCellDB-character-missing-method: 'data.frame'-like mutation/accessor generics for...

In CellaRepertorium: Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Description

A ContigCellDB pretend to be a cell_tbl data.frame in several regards. This is to enable nesting ContigCellDB objects in the colData of a SingleCellExperiment and so that various plotting functionality in scater can do something sensible.

Usage

## S4 method for signature 'ContigCellDB,character,missing'
x[[i, j, ...]]

## S4 method for signature 'ContigCellDB,ANY,missing,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'ContigCellDB'
dim(x)

## S4 method for signature 'ContigCellDB'
dimnames(x)

## S4 method for signature 'ContigCellDB'
nrow(x)

## S4 method for signature 'ContigCellDB'
ncol(x)

Arguments

x	ContigCellDB
i	integer or character index
j	ignored
...	ignored
drop	ignored

Details

If x a ContigCellDB, then dim(x) and dimnames(x) return dim(x$cell_tbl) and dimnames(x$cell_tbl), respectively, and x[[col]] returns x$cell_tbl[[col]]. Likewise indexing with x[i,] returns cells indexed by i. Finally as.data.frame(x) returns x$cell_tbl.

Value

See details.

Examples

 data(ccdb_ex)
 ccdb_ex[1:10,]
 head(ccdb_ex[['barcode']])
 dim(ccdb_ex)
 dimnames(ccdb_ex)

CellaRepertorium documentation built on Nov. 8, 2020, 7:48 p.m.