tests/testthat/_snaps/getSampleTileMatrix.md

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

getSampleTileMatrices works on a 1 sample test dataset

{
  "type": "integer",
  "attributes": {},
  "value": [25112, 1]
}

$summarizedData
class: SummarizedExperiment 
dim: 2 1 
metadata(0):
assays(18): CellCounts FragmentCounts ... ReadsInPeaks FRIP
rownames(2): C2 C5
rowData names(0):
colnames(1): PBMCSmall
colData names(2): Sample PassQC

$Genome
[1] "hg19"

$TxDb
$TxDb$pkgname
[1] "TxDb.Hsapiens.UCSC.hg19.knownGene"

$TxDb$metadata
                                       name
1                                   Db type
2                        Supporting package
3                               Data source
4                                    Genome
5                                  Organism
6                               Taxonomy ID
7                                UCSC Table
8                              Resource URL
9                           Type of Gene ID
10                             Full dataset
11                         miRBase build ID
12                          transcript_nrow
13                                exon_nrow
14                                 cds_nrow
15                            Db created by
16                            Creation time
17 GenomicFeatures version at creation time
18         RSQLite version at creation time
19                          DBSCHEMAVERSION
                                          value
1                                          TxDb
2                               GenomicFeatures
3                                          UCSC
4                                          hg19
5                                  Homo sapiens
6                                          9606
7                                     knownGene
8                       http://genome.ucsc.edu/
9                                Entrez Gene ID
10                                          yes
11                                       GRCh37
12                                        82960
13                                       289969
14                                       237533
15    GenomicFeatures package from Bioconductor
16 2015-10-07 18:11:28 +0000 (Wed, 07 Oct 2015)
17                                      1.21.30
18                                        1.0.0
19                                          1.1


$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


$Directory
[1] "/Users/imran.mcgrath/Documents/projects/PBMCSmall/MOCHA"

$History
$History[[1]]
[1] "callOpenTiles 1.0.2"

$History[[2]]
[1] "getSampleTileMatrix 1.0.2"

DataFrame with 1 row and 2 columns
               Sample    PassQC
          <character> <numeric>
PBMCSmall   PBMCSmall         1

MOCHA documentation built on May 29, 2024, 2:25 a.m.