View source: R/curatedTCGAData.R
curatedTCGAData | R Documentation |
curatedTCGAData assembles data on-the-fly from ExperimentHub
to provide cohesive MultiAssayExperiment container objects.
All the user has to do is to provide TCGA disease code(s) and assay types.
It is highly recommended to use the companion package TCGAutils
,
developed to work with TCGA data specifically from curatedTCGAData
and
some flat files.
curatedTCGAData(
diseaseCode = "*",
assays = "*",
version,
dry.run = TRUE,
verbose = TRUE,
...
)
diseaseCode |
character() A vector of TCGA cancer cohort codes
(e.g., |
assays |
character() A vector of TCGA assays, glob matches allowed; see below for more details |
version |
character(1) One of |
dry.run |
logical(1) Whether to return the dataset names before actual download (default TRUE) |
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. Only the latest runDate ("2016-01-28") is supported.
Use the dry.run = FALSE
to download remote datasets and
build an integrative MultiAssayExperiment object.
For a list of 'diseaseCodes', see the curatedTCGAData-package
help page.
a MultiAssayExperiment of the specified assays and
cancer codes or informative data.frame of resources when dry.run
is TRUE
Below is a list of partial ExperimentList
assay names and their respective
description. These assays can be entered as part of the assays
argument in the main function. Partial glob matches are allowed such as:
'CN*'
for "CNASeq", "CNASNP", "CNVSNP" assays. Credit: Ludwig G.
ExperimentList data types Description ---------------------------------------------------------------------------- SummarizedExperiment* RNASeqGene Gene expression values RNASeq2Gene RSEM TPM gene expression values RNASeq2GeneNorm Upper quartile log2 normalized RSEM TPM gene expression values miRNAArray Probe-level miRNA expression values miRNASeqGene Gene-level log2 RPM miRNA expression values mRNAArray Unified gene-level mRNA expression values mRNAArray_huex Gene-level mRNA expression values from Affymetrix Human Exon Array mRNAArray_TX_g4502a Gene-level mRNA expression values from Agilent 244K Array mRNAArray_TX_ht_hg_u133a Gene-level mRNA expression values from Affymetrix Human Genome U133 Array GISTIC_AllByGene Gene-level GISTIC2 copy number values GISTIC_ThresholdedByGene Gene-level GISTIC2 thresholded discrete copy number values RPPAArray Reverse Phase Protein Array normalized protein expression values RangedSummarizedExperiment GISTIC_Peaks GISTIC2 thresholded discrete copy number values in recurrent peak regions SummarizedExperiment with HDF5Array DelayedMatrix Methylation_methyl27 Probe-level methylation beta values from Illumina HumanMethylation 27K BeadChip Methylation_methyl450 Probe-level methylation beta values from Infinium HumanMethylation 450K BeadChip RaggedExperiment CNASNP Segmented somatic Copy Number Alteration calls from SNP array CNVSNP Segmented germline Copy Number Variant calls from SNP Array CNASeq Segmented somatic Copy Number Alteration calls from low pass DNA Sequencing Mutation* Somatic mutations calls CNACGH_CGH_hg_244a Segmented somatic Copy Number Alteration calls from CGH Agilent Microarray 244A CNACGH_CGH_hg_415k_g4124a Segmented somatic Copy Number Alteration calls from CGH Agilent Microarray 415K * All can be converted to RangedSummarizedExperiment (except RPPAArray) with TCGAutils
Version 2.1.1
provides a couple of corrections to the colData
for ovarian
cancer (OV
) and skin cancer (SKCM
). In these new data, the cancer
subtype variables are fully available. One get obtain the mapping of columns
to subtypes in the colData
with the getSubtypeMap
function in
TCGAutils
.
Version 2.1.0
provides gene-level log2 RPM miRNA expression values for
miRNASeqGene
data log2 normalized RSEM for RNASeq2GeneNorm
assays.
Previously, the data provided were read counts and normalized counts,
respectively. See issue #53 on GitHub for
additional details.
The new version 2.0.1
includes various improvements including an
additional assay that provides RNASeq2Gene
data as RSEM TPM gene
expression values (issue #38). Additional changes include genomic
information for RaggedExperiment
type data objects where '37' is now
'GRCh37' as reported in issue #40. Datasets (e.g., OV, GBM) that contain
multiple assays that could be merged are now provided as merged assays
(issue #27). We corrected an issue where mRNAArray
assays were returning
DataFrame
s instead of matrix
type data (issue #31). Version 1.1.38
provides the original run of curatedTCGAData
and is provided due to legacy
reasons.
curatedTCGAData-package
curatedTCGAData(
diseaseCode = c("GBM", "ACC"), assays = "CNASNP", version = "2.0.1"
)
curatedTCGAData("BRCA", "GISTIC*", "2.0.1")
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