getLinkedOmicsData: Retrieve linkedOmics data

Description Usage Arguments Value Examples

View source: R/linkedOmics.R

Description

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

Usage

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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

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## 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.