getPCa: Construct Prostate Cancer MultiAssayExperiment object from...

In Syksy/curatedPCaData: Curated Prostate Cancer Data

Construct Prostate Cancer MultiAssayExperiment object from specific cohort

Description

curatedPCaData provides MultiAssayExperiment container objects that are constructed from ExperimentHub. User provides PCa dataset name (see list on the overview-vignette or help files).

Usage

getPCa(dataset, assays, timestamp, sampletypes, verbose = FALSE, ...)

Arguments

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 ExperimentHub constructor

Details

This function will check against available resources in ExperimentHub. For a list of datasets, see the overview-vignette or below dataset listing.

Value

a MultiAssayExperiment of the specified assays and cancer cohort

Available datasets

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.

Available Assays

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.

timestamp

"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".

See Also

curatedPCaData-package

Examples

mae_taylor <- getPCa(
    dataset = "taylor", timestamp = "20230215"
)

Syksy/curatedPCaData documentation built on Nov. 4, 2023, 9:46 a.m.