Access and assignment methods for muscadet objects

Simplified access to omic datasets and slots inside muscadet objects.

Assign new data in a [muscadet::muscadet()] or [muscadet::muscomic()] object. For muscadet objects, the omic datasets in the omics slot can be directly reassigned.

Usage

# S3 method for class 'muscadet'
x[i, ...]

# S3 method for class 'muscomic'
x[i, ...]

# S3 method for class 'muscadet'
x$name

# S3 method for class 'muscomic'
x$name

# S3 method for class 'muscadet'
x[i] <- value

# S3 method for class 'muscomic'
x[i] <- value

# S3 method for class 'muscadet'
x$i <- value

# S3 method for class 'muscomic'
x$i <- value

Arguments

x: A muscadet or muscomic object.
i: The name of the slot (or omic).
...: Other arguments (ignored).
name: The name of the slot (or omic).
value: The new value to assign.

Value

The selected slot or the omic dataset ([muscadet::muscomic()] object) for muscadet objects. The selected slot for muscomic objects.

The updated [muscadet::muscadet()] or [muscadet::muscomic()] object.

Examples

# Load example muscadet object
# data("exdata_muscadet")

# Access to muscadet omics or slots
exdata_muscadet["ATAC"]
#> A muscomic object 
#>  type: ATAC 
#>  label: scATAC-seq 
#>  cells: 71 
#>  counts: 71 cells x 1200 features (peaks)
#>  logratio: 71 cells x 213 features (windows of peaks)
#>  variant positions: 681
exdata_muscadet["genome"]
#> [1] "hg38"

# Load example muscadet object
# data("exdata_muscadet")

# Access to muscomic slots
exdata_muscadet["ATAC"]["label.omic"]
#> [1] "scATAC-seq"

# Load example muscadet object
# data("exdata_muscadet")

# Access to muscadet omics or slots
exdata_muscadet$ATAC
#> A muscomic object 
#>  type: ATAC 
#>  label: scATAC-seq 
#>  cells: 71 
#>  counts: 71 cells x 1200 features (peaks)
#>  logratio: 71 cells x 213 features (windows of peaks)
#>  variant positions: 681
exdata_muscadet$genome
#> [1] "hg38"

# Load example muscadet object
# data("exdata_muscadet")

# Access to muscomic slots
exdata_muscadet$ATAC$label.omic
#> [1] "scATAC-seq"

# Load example muscadet object
# data("exdata_muscadet")

# Assign new data in muscadet object
exdata_muscadet["genome"] <- "hg38"

# Load example muscadet object
# data("exdata_muscadet")

# Assign new data in muscomic object
exdata_muscadet["ATAC"]["label.omic"] <- "scATAC-seq"

# Load example muscadet object
# data("exdata_muscadet")

# Assign new data in muscadet object
exdata_muscadet$genome <- "hg38"

# Load example muscadet object
# data("exdata_muscadet")

# Assign new data in muscomic object
exdata_muscadet$ATAC$label.omic <- "scATAC-seq"