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("exdata_muscadet")

exdata_muscadet
#> A muscadet object 
#>  2 omics: ATAC, RNA 
#>  types: ATAC, RNA 
#>  labels: scATAC-seq, scRNA-seq 
#>  cells: 71, 69 (common: 63, total: 77) 
#>  counts: 71 cells x 1200 features (peaks), 69 cells x 300 features (genes) 
#>  logratio: 71 cells x 213 features (windows of peaks), 69 cells x 212 features (genes) 
#>  variant positions: 681, 359 
#>  bulk data: WGS 
#>  clustering: partitions = 0.1, 0.3, 0.5 ; optimal partition = 0.5 
#>  CNA calling: 2 clusters ; 3 consensus segments including 0 CNA segments 
#>  genome: hg38 

str(exdata_muscadet, 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 20
#>   ..@ genome    : chr "hg38"