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

We can call peaks independent of ArchR

Code
  tiles@metadata
Output
  $summarizedData
  class: SummarizedExperiment 
  dim: 2 1 
  metadata(0):
  assays(3): CellCounts FragmentCounts nFrags
  rownames(2): C2 C5
  rowData names(0):
  colnames(1): PBMCSmall
  colData names(1): Sample

  $Genome
  [1] "hg19"

  $TxDb
  $TxDb$pkgname
  [1] "TxDb.Hsapiens.UCSC.hg38.refGene"

  $TxDb$metadata
                                         name
  1                                   Db type
  2                        Supporting package
  3                               Data source
  4                                    Genome
  5                                  Organism
  6                               Taxonomy ID
  7                                UCSC Table
  8                                UCSC Track
  9                              Resource URL
  10                          Type of Gene ID
  11                             Full dataset
  12                         miRBase build ID
  13                        Nb of transcripts
  14                            Db created by
  15                            Creation time
  16 GenomicFeatures version at creation time
  17         RSQLite version at creation time
  18                          DBSCHEMAVERSION
                                            value
  1                                          TxDb
  2                               GenomicFeatures
  3                                          UCSC
  4                                          hg38
  5                                  Homo sapiens
  6                                          9606
  7                                       refGene
  8                                   NCBI RefSeq
  9                       http://genome.ucsc.edu/
  10                               Entrez Gene ID
  11                                          yes
  12                                         <NA>
  13                                        88816
  14    GenomicFeatures package from Bioconductor
  15 2021-04-28 16:30:46 +0000 (Wed, 28 Apr 2021)
  16                                       1.41.3
  17                                        2.2.6
  18                                          1.2


  $OrgDb
  $OrgDb$pkgname
  [1] "org.Hs.eg.db"

  $OrgDb$metadata
                   name                                                 value
  1     DBSCHEMAVERSION                                                   2.1
  2             Db type                                                 OrgDb
  3  Supporting package                                         AnnotationDbi
  4            DBSCHEMA                                              HUMAN_DB
  5            ORGANISM                                          Homo sapiens
  6             SPECIES                                                 Human
  7        EGSOURCEDATE                                            2021-Sep13
  8        EGSOURCENAME                                           Entrez Gene
  9         EGSOURCEURL                  ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
  10          CENTRALID                                                    EG
  11              TAXID                                                  9606
  12       GOSOURCENAME                                         Gene Ontology
  13        GOSOURCEURL http://current.geneontology.org/ontology/go-basic.obo
  14       GOSOURCEDATE                                            2021-09-01
  15     GOEGSOURCEDATE                                            2021-Sep13
  16     GOEGSOURCENAME                                           Entrez Gene
  17      GOEGSOURCEURL                  ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
  18     KEGGSOURCENAME                                           KEGG GENOME
  19      KEGGSOURCEURL                  ftp://ftp.genome.jp/pub/kegg/genomes
  20     KEGGSOURCEDATE                                            2011-Mar15
  21       GPSOURCENAME             UCSC Genome Bioinformatics (Homo sapiens)
  22        GPSOURCEURL                                                      
  23       GPSOURCEDATE                                            2021-Jul20
  24       ENSOURCEDATE                                            2021-Apr13
  25       ENSOURCENAME                                               Ensembl
  26        ENSOURCEURL               ftp://ftp.ensembl.org/pub/current_fasta
  27       UPSOURCENAME                                               Uniprot
  28        UPSOURCEURL                               http://www.UniProt.org/
  29       UPSOURCEDATE                              Wed Sep 15 18:21:59 2021


  $History
  $History[[1]]
  [1] "callOpenTiles 1.1.0"