subsetMOCHAObject.md
In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

We can subset a tileResults object by celltypes

A MultiAssayExperiment object of 1 listed
 experiment with a user-defined name and respective class.
 Containing an ExperimentList class object of length 1:
 [1] C3: RaggedExperiment with 50000 rows and 3 columns
Functionality:
 experiments() - obtain the ExperimentList instance
 colData() - the primary/phenotype DataFrame
 sampleMap() - the sample coordination DataFrame
 `$`, `[`, `[[` - extract colData columns, subset, or experiment
 *Format() - convert into a long or wide DataFrame
 assays() - convert ExperimentList to a SimpleList of matrices
 exportClass() - save data to flat files

class: SummarizedExperiment 
dim: 1 3 
metadata(0):
assays(16): CellCounts FragmentCounts ... DoubletEnrichment
  BlacklistRatio
rownames(1): C3
rowData names(0):
colnames(3): scATAC_BMMC_R1 scATAC_CD34_BMMC_R1 scATAC_PBMC_R1
colData names(2): Sample PassQC

We can subset a tileResults object by Sample grouping

A MultiAssayExperiment object of 2 listed
 experiments with user-defined names and respective classes.
 Containing an ExperimentList class object of length 2:
 [1] C2: RaggedExperiment with 50000 rows and 1 columns
 [2] C3: RaggedExperiment with 50000 rows and 1 columns
Functionality:
 experiments() - obtain the ExperimentList instance
 colData() - the primary/phenotype DataFrame
 sampleMap() - the sample coordination DataFrame
 `$`, `[`, `[[` - extract colData columns, subset, or experiment
 *Format() - convert into a long or wide DataFrame
 assays() - convert ExperimentList to a SimpleList of matrices
 exportClass() - save data to flat files

class: SummarizedExperiment 
dim: 2 1 
metadata(0):
assays(16): CellCounts FragmentCounts ... DoubletEnrichment
  BlacklistRatio
rownames(2): C2 C3
rowData names(0):
colnames(1): scATAC_CD34_BMMC_R1
colData names(2): Sample PassQC