The muscadet class

A muscadet object encapsulates data from different single-cell omics as muscomic objects as well as downstream analysis results after clustering and CNA calling.

Slots

omics

List of muscomic objects, one per single-cell omic (list).

bulk.data

List of objects containing data from paired bulk sequencing (list).

clustering

List of objects containing data associated with the clustering of cells based on coverage log R ratio values (list).

cnacalling

List of objects containing data associated with the calling of copy number alterations (CNAs) (list).

genome

Reference genome name among: "hg38", "hg19" and "mm10" (character).

See also

Functions related to muscadet objects:

• CreateMuscadetObject() (create muscadet objects)

• muscadet-access (simplified access and assignment methods)

• .DollarNames.muscadet (autocompletion for $)

• show,muscadet-method (show method)

Examples

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

muscadet_obj
#> A muscadet object 
#>  2 omics: ATAC, RNA 
#>  types: ATAC, RNA 
#>  labels: scATAC-seq, scRNA-seq 
#>  coverage data matrix: log.ratio, log.ratio 
#>  cells: 112, 119 (common: 84, total: 147) 
#>  features: 133, 349 
#>  feature labels: windows of peaks, genes 
#>  variant positions: 691, 373 
#>  data from paired bulk sequencing: WGS 
#>  clustering: partitions = 0.6, 0.8, 1 ; optimal partition = 1 
#>  CNA calling: 2 clusters ; 47 consensus segments including 1 CNA segments 
#>  genome: hg38 

str(muscadet_obj, max.level = 2)
#> Formal class 'muscadet' [package "muscadet"] with 5 slots
#>   ..@ omics     :List of 2
#>   ..@ bulk.data :List of 2
#>   ..@ clustering:List of 9
#>   ..@ cnacalling:List of 21
#>   ..@ genome    : chr "hg38"