To merge the list elements returned from curatedMetagenomicData into a
single
SummarizedExperiment or
TreeSummarizedExperiment
object, users will use mergeData() provided elements are the same
dataType (see returnSamples). This is useful for analysis across entire
studies (e.g. meta-analysis); however, when doing analysis across individual
samples (e.g. mega-analysis) returnSamples is preferable.
Arguments
- mergeList
a
listreturned from curatedMetagenomicData where all of the elements are of the samedataType(see returnSamples)
Value
when mergeList elements are of dataType (see returnSamples)
relative_abundance, a
TreeSummarizedExperiment
object is returned; otherwise, a
SummarizedExperiment
object is returned
Details
Internally, mergeData() must full join assays and rowData slots of each
SummarizedExperiment or
TreeSummarizedExperiment
object (colData is merged slightly more efficiently by row binding). While
dplyr methods are used for maximum efficiency, users should be aware that
memory requirements can be large when merging many list elements.
Examples
curatedMetagenomicData("LiJ_20.+.marker_abundance", dryrun = FALSE) |>
mergeData()
#> class: SummarizedExperiment
#> dim: 77729 456
#> metadata(0):
#> assays(1): marker_abundance
#> rownames(77729): 39491__A0A395UVM9__DXB76_04540
#> 39491__A0A395UZL1__DXB76_05950 ... 1262937__R7LHU6__BN805_01557
#> 712117__F3PBR4__HMPREF9056_02502
#> rowData names(0):
#> colnames(456): DLF005-IE DLM006-IE ... nHM612836 nHMX11726
#> colData names(28): study_name subject_id ... location smoker
curatedMetagenomicData("LiJ_20.+.pathway_abundance", dryrun = FALSE) |>
mergeData()
#> class: SummarizedExperiment
#> dim: 27110 456
#> metadata(0):
#> assays(1): pathway_abundance
#> rownames(27110): UNMAPPED UNINTEGRATED ... PWY-7539:
#> 6-hydroxymethyl-dihydropterin diphosphate biosynthesis III
#> (Chlamydia)|g__Prevotella.s__Prevotella_buccae LACTOSECAT-PWY:
#> lactose and galactose degradation
#> I|g__Escherichia.s__Escherichia_coli
#> rowData names(0):
#> colnames(456): DLF005-IE DLM006-IE ... nHM612836 nHMX11726
#> colData names(28): study_name subject_id ... location smoker
curatedMetagenomicData("LiJ_20.+.relative_abundance", dryrun = FALSE) |>
mergeData()
#>
#> $`2021-03-31.LiJ_2014.relative_abundance`
#> dropping rows without rowTree matches:
#> k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella_profusa
#> k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#> k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella]_massiliensis
#> k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales_unclassified|g__Gemella|s__Gemella_bergeri
#> k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella_elegans
#> k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#> k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia_extructa
#> k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#> k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus_evryensis
#> $`2021-10-14.LiJ_2017.relative_abundance`
#> dropping rows without rowTree matches:
#> k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#> k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#> k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#> k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus_evryensis
#> class: TreeSummarizedExperiment
#> dim: 691 456
#> metadata(0):
#> assays(1): relative_abundance
#> rownames(691):
#> k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_plebeius
#> k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_caccae
#> ...
#> k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria_elongata
#> k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia_alcalifaciens
#> rowData names(7): superkingdom phylum ... genus species
#> colnames(456): DLF005-IE DLM006-IE ... nHM612836 nHMX11726
#> colData names(28): study_name subject_id ... location smoker
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (691 rows)
#> rowTree: 1 phylo tree(s) (10430 leaves)
#> colLinks: NULL
#> colTree: NULL