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

We can subset a sampleTileMatrix object by celltypes

class: RangedSummarizedExperiment 
dim: 22773 3 
metadata(6): summarizedData Genome ... Directory History
assays(1): C3
rownames(22773): chr10:100028000-100028499 chr10:100080500-100080999
  ... chrY:2709500-2709999 chrY:2803000-2803499
rowData names(2): C2 C3
colnames(3): scATAC_BMMC_R1 scATAC_CD34_BMMC_R1 scATAC_PBMC_R1
colData names(2): Sample PassQC

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 sampleTileMatrix object by Sample

class: RangedSummarizedExperiment 
dim: 22773 1 
metadata(6): summarizedData Genome ... Directory History
assays(2): C2 C3
rownames(22773): chr10:100028000-100028499 chr10:100080500-100080999
  ... chrY:2709500-2709999 chrY:2803000-2803499
rowData names(2): C2 C3
colnames(1): scATAC_CD34_BMMC_R1
colData names(2): Sample PassQC

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