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("exdata_muscadet")

exdata_muscadet$ATAC
#> A muscomic object 
#>  type: ATAC 
#>  label: scATAC-seq 
#>  cells: 71 
#>  counts: 71 cells x 1200 features (peaks)
#>  logratio: 71 cells x 213 features (windows of peaks)
#>  variant positions: 681
exdata_muscadet$RNA
#> A muscomic object 
#>  type: RNA 
#>  label: scRNA-seq 
#>  cells: 69 
#>  counts: 69 cells x 300 features (genes)
#>  logratio: 69 cells x 212 features (genes)
#>  variant positions: 359

str(exdata_muscadet$ATAC, max.level = 2)
#> Formal class 'muscomic' [package "muscadet"] with 4 slots
#>   ..@ type      : chr "ATAC"
#>   ..@ label.omic: chr "scATAC-seq"
#>   ..@ coverage  :List of 2
#>   ..@ allelic   :List of 3