getLinkedOmicsData: Retrieve linkedOmics data

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Description

Retrieve linkedOmics data from http://linkedomics.org/

Usage

getLinkedOmicsData(project, dataset)

Arguments

project

A linkedOmics project: TCGA-ACC TCGA-BLCA TCGA-BRCA TCGA-CESC TCGA-CHOL TCGA-COADREAD TCGA-DLBC TCGA-ESCA TCGA-GBM TCGA-GBMLGG TCGA-HNSC TCGA-KICH TCGA-KIPAN TCGA-KIRC TCGA-KIRP TCGA-LAML TCGA-LGG TCGA-LIHC TCGA-LUAD TCGA-LUSC TCGA-MESO TCGA-OV TCGA-PAAD TCGA-PCPG TCGA-PRAD TCGA-SARC TCGA-SKCM TCGA-STAD TCGA-STES TCGA-TGCT TCGA-THCA TCGA-THYM TCGA-UCEC TCGA-UCS TCGA-UVM CPTAC-COAD

dataset

A dataset from the list below Annotated mutation Clinical Glycoproteome (Gene level) Glycoproteome (Site level) Methylation (CpG-site level, HM27) Methylation (CpG-site level, HM450K) Methylation (Gene level, HM27) Methylation (Gene level, HM450K) miRNA (GA, Gene level) miRNA (GA, Isoform level) miRNA (GA, miRgene level) miRNA (Gene level) miRNA (HiSeq, Gene level) miRNA (HiSeq, miRgene level) miRNA (isoform level) miRNA (miRgene level) Mutation (Gene level) Mutation (Site level) Mutation raw file (Somatic and MSIndel) Phosphoproteome (Gene level) Phosphoproteome (Site level) Phosphoproteomics (Normal) Phosphoproteomics (Tumor) Proteome (Gene level) Proteome (Gene Level) Proteome (JHU, Gene level) Proteome (PNNL, Gene level, Normal TMT Unshared Log Ratio) Proteome (PNNL, Gene level, Tumor TMT Unshared Log Ratio) Proteome (PNNL, Gene level) Proteome (VU, Gene level, Label-free Unshared Counts) RNAseq (GA, Gene level) RNAseq (HiSeq, Gene level) RPPA (Analyte level) RPPA (Analyte Level) RPPA (Gene level) RPPA (Gene Level) SCNV (Focal level, log-ratio) SCNV (Focal level, Thresholded) SCNV (Gene level, log ratio) SCNV (Gene level, log-ratio) SCNV (Gene level, Thresholded) SCNV (Segment level)

Value

A matrix with the data

Examples

## Not run: 
TCGA_COAD_protein <- getLinkedOmicsData(
  project = "TCGA-COADREAD",
  dataset = "Proteome (Gene level)"
)
TCGA_COAD_RNASeq_hiseq <- getLinkedOmicsData(
  project = "TCGA-COADREAD",
  dataset = "RNAseq (HiSeq, Gene level)"
)
TCGA_COAD_RNASeq_ga <- getLinkedOmicsData(
  project = "TCGA-COADREAD",
  dataset = "RNAseq (GA, Gene level)"
)
TCGA_COAD_RPPA <- getLinkedOmicsData(
  project = "TCGA-COADREAD",
  dataset = "RPPA (Gene level)"
)

## End(Not run)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.