load all compendium data into a TreeSummarizedExperiment

Usage

getCompendium(bfc = BiocFileCache::BiocFileCache())

Arguments

bfc: BiocFileCache object to use

Value

a `TreeSummarizedExperiment`

Examples

cpd <- getCompendium()

dim(cpd)
#> [1]   4018 168464
cpd
#> class: TreeSummarizedExperiment 
#> dim: 4018 168464 
#> metadata(0):
#> assays(1): counts
#> rownames(4018):
#>   Bacteria.Firmicutes.Clostridia.Oscillospirales.Ruminococcaceae.Subdoligranulum
#>   Bacteria.Proteobacteria.Gammaproteobacteria.Burkholderiales.Alcaligenaceae.Achromobacter
#>   ...
#>   Bacteria.Proteobacteria.Alphaproteobacteria.Rhodobacterales.Rhodobacteraceae.Poseidonocella
#>   Bacteria.CK-2C2-2.NA.NA.NA.NA
#> rowData names(8): kingdom phylum ... species strain
#> colnames(168464): PRJDB10485_DRR243823 PRJDB10485_DRR243824 ...
#>   PRJNA764337_SRR15959628 PRJNA764337_SRR15959674
#> colData names(11): srs project ... iso region
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: NULL
#> rowTree: NULL
#> colLinks: NULL
#> colTree: NULL
assayNames(cpd)
#> [1] "counts"
head(colData(cpd))
#> DataFrame with 6 rows and 11 columns
#>                              srs     project         srr library_strategy
#>                      <character> <character> <character>      <character>
#> PRJDB10485_DRR243823   DRS176859  PRJDB10485   DRR243823         AMPLICON
#> PRJDB10485_DRR243824   DRS176860  PRJDB10485   DRR243824         AMPLICON
#> PRJDB10485_DRR243825   DRS176861  PRJDB10485   DRR243825         AMPLICON
#> PRJDB10485_DRR243826   DRS176862  PRJDB10485   DRR243826         AMPLICON
#> PRJDB10485_DRR243827   DRS176863  PRJDB10485   DRR243827         AMPLICON
#> PRJDB10485_DRR243828   DRS176864  PRJDB10485   DRR243828         AMPLICON
#>                      library_source             pubdate total_bases
#>                         <character>           <POSIXct> <integer64>
#> PRJDB10485_DRR243823    METAGENOMIC 2021-03-26 15:30:38    85432160
#> PRJDB10485_DRR243824    METAGENOMIC 2021-03-26 15:30:40    85497094
#> PRJDB10485_DRR243825    METAGENOMIC 2021-03-26 15:30:40    81068656
#> PRJDB10485_DRR243826    METAGENOMIC 2021-03-26 15:30:40    72020224
#> PRJDB10485_DRR243827    METAGENOMIC 2021-03-26 15:30:40    81402358
#> PRJDB10485_DRR243828    METAGENOMIC 2021-03-26 15:30:40    83867024
#>                          instrument    geo_loc_name         iso
#>                         <character>     <character> <character>
#> PRJDB10485_DRR243823 Illumina MiSeq ghana:koforidua          GH
#> PRJDB10485_DRR243824 Illumina MiSeq ghana:koforidua          GH
#> PRJDB10485_DRR243825 Illumina MiSeq ghana:koforidua          GH
#> PRJDB10485_DRR243826 Illumina MiSeq ghana:koforidua          GH
#> PRJDB10485_DRR243827 Illumina MiSeq ghana:koforidua          GH
#> PRJDB10485_DRR243828 Illumina MiSeq ghana:koforidua          GH
#>                                  region
#>                             <character>
#> PRJDB10485_DRR243823 Sub-Saharan Africa
#> PRJDB10485_DRR243824 Sub-Saharan Africa
#> PRJDB10485_DRR243825 Sub-Saharan Africa
#> PRJDB10485_DRR243826 Sub-Saharan Africa
#> PRJDB10485_DRR243827 Sub-Saharan Africa
#> PRJDB10485_DRR243828 Sub-Saharan Africa