assays of SummarizedExperiments coming as DataFrame (why not matrix?)
lgeistlinger opened this issue · 1 comments
lgeistlinger commented
ov.ctd <- curatedTCGAData(diseaseCode="OV", assays="mRNAArray*", dry.run=FALSE)
ov.ctd
A MultiAssayExperiment object of 4 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 4:
[1] OV_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 575 columns
[2] OV_mRNAArray_TX_g4502a_1-20160128: SummarizedExperiment with 17814 rows and 546 columns
[3] OV_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 31 columns
[4] OV_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 524 columns
Features:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample availability DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
> class(assay(ov.ctd[[1]]))
[1] "DataFrame"
attr(,"package")
[1] "S4Vectors"
> assay(ov.ctd[[1]])[1:5,1:5]
DataFrame with 5 rows and 5 columns
TCGA-04-1331-01A-01R-0435-03 TCGA-04-1332-01A-01R-0435-03
<numeric> <numeric>
C9orf152 5.1293974840562 4.03686128489381
ELMO2 7.3984111313982 7.89992552704923
RPS11 10.4792357981549 10.6598180297217
CREB3L1 6.59814293845376 7.12543317829795
PNMA1 8.68896823329707 8.81371426777574
TCGA-04-1335-01A-01R-0435-03 TCGA-04-1336-01A-01R-0435-03
<numeric> <numeric>
C9orf152 6.66831554256062 5.44171019721024
ELMO2 7.50944968310899 6.67400849392619
RPS11 10.2811624348218 10.4212441826243
CREB3L1 6.79374925015387 5.62442668141407
PNMA1 8.0662892719799 8.59987516862962
TCGA-04-1337-01A-01R-0435-03
<numeric>
C9orf152 3.48762601212778
ELMO2 8.6307994685934
RPS11 10.2659952571456
CREB3L1 7.11216823651922
PNMA1 8.37578982646659
I would expect those as a numeric matrix. What's the rationale behind providing them as a DataFrame?