The muscomic class

A muscomic object encapsulates coverage and allelic data from one single-cell omic dataset used as primary input for muscadet analysis.

Slots

type

Type of single-cell omic. Either ATAC or RNA currently supported (character).

label.omic

Label to display for the single-cell omic (character).

coverage

Coverage data on features (list).

allelic

Allelic data at variant positions (common SNPs or individual-specific heterozygous positions) (list).

See also

Functions related to muscomic objects:

• CreateMuscomicObject() (create muscomic objects)

• muscadet-access (simplified access and assignment methods)

• .DollarNames.muscadet (autocompletion for $)

• show,muscomic-method (show method)

Examples

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

muscadet_obj$ATAC
#> A muscomic object of type ATAC labelled scATAC-seq containing: 
#>  log.ratio coverage data matrix 
#>  112 cells 
#>  133 features: windows of peaks 
#>  691 variant positions 
muscadet_obj$RNA
#> A muscomic object of type RNA labelled scRNA-seq containing: 
#>  log.ratio coverage data matrix 
#>  119 cells 
#>  349 features: genes 
#>  373 variant positions 

str(muscadet_obj$ATAC, max.level = 2)
#> Formal class 'muscomic' [package "muscadet"] with 4 slots
#>   ..@ type      : chr "ATAC"
#>   ..@ label.omic: chr "scATAC-seq"
#>   ..@ coverage  :List of 6
#>   ..@ allelic   :List of 1