getPCa | R Documentation |
curatedPCaData provides MultiAssayExperiment container objects that are constructed from ExperimentHub. User provides PCa dataset name (see list on the overview-vignette or help files).
getPCa(dataset, assays, timestamp, sampletypes, verbose = FALSE, ...)
dataset |
character() of PCa cancer cohort names (e.g., 'abida') |
assays |
character() A vector of PCa assays. If not included, returns all available for the selected dataset; see below for more details. |
timestamp |
character(1) "20230215" indicating the data version to obtain from 'ExperimentHub'. See 'timestamp' section details. |
sampletypes |
A character vector of sample types to include in the MAE. If the parameter is missing, then all samples are returned. Allowed values are: 'primary', 'metastatic', 'normal', 'BPH', 'atrophic' |
verbose |
logical(1) Whether to show the dataset currenlty being (down)loaded (default TRUE) |
... |
Additional arguments passed on to the
|
This function will check against available resources in ExperimentHub. For a list of datasets, see the overview-vignette or below dataset listing.
a MultiAssayExperiment of the specified assays and cancer cohort
Following shortnames can be used with getPCa to query for their omics from ExperimentHub. For more detailed description of the studies, see their corresponding R documentation file. Further details are reported in the overview-vignette.
Shortname Rd documentation file Longer name(s) ---------------------------------------------------------------------------- abida curatedPCaDatasets_abida Abida et al. baca curatedPCaDatasets_baca Baca et al. barbieri curatedPCaDatasets_barbieri Barbieri et al. barwick curatedPCaDatasets_barwick Barwick et al. chandran curatedPCaDatasets_chandran Chandran et al., Yu et al. friedrich curatedPCaDatasets_friedrich Friedrich et al. hieronymus curatedPCaDatasets_hieronymus Hieronymus et al. icgcca curatedPCaDatasets_icgcca ICGC Canadian subset igc curatedPCaDatasets_igc International Genomics Consortium (PCa subset) kim curatedPCaDatasets_kim Kim et al. kunderfranco curatedPCaDatasets_kunderfranco Kunderfranco et al. ren curatedPCaDatasets_ren Ren et al. sun curatedPCaDatasets_sun Sun et al. taylor curatedPCaDatasets_taylor Taylor et al. tcga curatedPCaDatasets_tcga The Cancer Genome Atlas (PCa subset, PRAD-prefix) true curatedPCaDatasets_true True et al. wallace curatedPCaDatasets_wallace Wallace et al. wang curatedPCaDatasets_wang Wang et al. weiner curatedPCaDatasets_weiner Weiner et al.
The list of ExperimentList assay names and their descriptions.
These assays can be entered as part of the assays
argument in the
main function.
ExperimentList data types Description ---------------------------------------------------------------------------- gex.rma Gene expression values (RMA normalized) gex.logq (Log-quantile) gex.relz (Relative z-scores) gex.logr (Log-ratios) gex.rsem.log (Log-RSEM) cna.gistic Copy number alteration (GISTIC calls) cna.logr (Log-ratios) mut Somatic mutation calls cibersort Immune deconvolution as estimated by CIBERSORTx xcell xCell epic EPIC quantiseq quanTIseq mcp MCP-counter estimate ESTIMATE scores Various risk and AR scores; see vignette references.
"20230215" The timestamp is updated in case the data is updated. In this case, this section describes the changes made for new timestamps. At this time, the only data deposit is from 2023, Feb 15th, indicated by "20230215".
curatedPCaData-package
mae_taylor <- getPCa(
dataset = "taylor", timestamp = "20230215"
)
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