linkedOmics parsing tables

1 Install packages

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

2 Load packages

library(TCGAbiolinksGUI.data)
library(TCGAbiolinks)
library(dplyr)

3 Parsing links results

data('linkedOmics.data')
linkedOmics.data %>% 
    select(c("project","OMICS Dataset","Unit","Samples","Atrributes","url")) %>% 
    DT::datatable(style = "bootstrap",
                  filter = "top",
                  options = list(scrollX = TRUE,
                                 pageLength = 5, 
                                 autoWidth = TRUE)) %>%
  DT::formatStyle(columns = colnames(.), fontSize = '50%')

4 COAD Dataset

4.1 Linked OMics

TCGA_COAD_protein <- getLinkedOmicsData(project = "TCGA-COADREAD",dataset = "Proteome (Gene level)")
dim(TCGA_COAD_protein)

## [1] 5538   91

TCGA_COAD_RNASeq_hiseq <- getLinkedOmicsData(project = "TCGA-COADREAD",dataset = "RNAseq (HiSeq, Gene level)")
dim(TCGA_COAD_RNASeq_hiseq)

## [1] 19828   380

TCGA_COAD_RNASeq_ga <- getLinkedOmicsData(project = "TCGA-COADREAD",dataset = "RNAseq (GA, Gene level)")
dim(TCGA_COAD_RNASeq_ga)

## [1] 6149  223

TCGA_COAD_RPPA <- getLinkedOmicsData(project = "TCGA-COADREAD",dataset = "RPPA (Gene level)")
dim(TCGA_COAD_RPPA)

## [1] 159 492

intersect(colnames(TCGA_COAD_protein),colnames(TCGA_COAD_RNASeq_ga))

##  [1] "attrib_name"  "TCGA.A6.3807" "TCGA.A6.3808" "TCGA.A6.3810" "TCGA.AA.3518"
##  [6] "TCGA.AA.3525" "TCGA.AA.3526" "TCGA.AA.3529" "TCGA.AA.3531" "TCGA.AA.3534"
## [11] "TCGA.AA.3552" "TCGA.AA.3554" "TCGA.AA.3558" "TCGA.AA.3561" "TCGA.AA.3664"
## [16] "TCGA.AA.3666" "TCGA.AA.3672" "TCGA.AA.3684" "TCGA.AA.3710" "TCGA.AA.3715"
## [21] "TCGA.AA.3818" "TCGA.AA.3848" "TCGA.AA.3864" "TCGA.AA.3986" "TCGA.AA.3989"
## [26] "TCGA.AA.A004" "TCGA.AA.A00A" "TCGA.AA.A00E" "TCGA.AA.A00F" "TCGA.AA.A00J"
## [31] "TCGA.AA.A00K" "TCGA.AA.A00N" "TCGA.AA.A00O" "TCGA.AA.A00R" "TCGA.AA.A00U"
## [36] "TCGA.AA.A010" "TCGA.AA.A017" "TCGA.AA.A01C" "TCGA.AA.A01D" "TCGA.AA.A01F"
## [41] "TCGA.AA.A01I" "TCGA.AA.A01K" "TCGA.AA.A024" "TCGA.AA.A029" "TCGA.AA.A02E"
## [46] "TCGA.AA.A02H" "TCGA.AA.A02J" "TCGA.AA.A02R" "TCGA.AF.2691" "TCGA.AF.2692"
## [51] "TCGA.AF.3400" "TCGA.AF.3913" "TCGA.AG.3574" "TCGA.AG.3580" "TCGA.AG.3584"
## [56] "TCGA.AG.3593" "TCGA.AG.3594" "TCGA.AG.4007" "TCGA.AG.A002" "TCGA.AG.A008"
## [61] "TCGA.AG.A00C" "TCGA.AG.A00H" "TCGA.AG.A00Y" "TCGA.AG.A011" "TCGA.AG.A014"
## [66] "TCGA.AG.A015" "TCGA.AG.A016" "TCGA.AG.A01J" "TCGA.AG.A01L" "TCGA.AG.A01N"
## [71] "TCGA.AG.A026" "TCGA.AG.A02X" "TCGA.AG.A032"

intersect(colnames(TCGA_COAD_protein),colnames(TCGA_COAD_RNASeq_hiseq))

## [1] "attrib_name"  "TCGA.AA.3526" "TCGA.AA.A01P" "TCGA.AA.A01X" "TCGA.AA.A01Z"
## [6] "TCGA.AA.A02Y"

intersect(colnames(TCGA_COAD_protein),colnames(TCGA_COAD_RNASeq_ga)) %>% length

## [1] 73

intersect(colnames(TCGA_COAD_protein),colnames(TCGA_COAD_RNASeq_hiseq))  %>% length

## [1] 6

4.2 TCGA

query.rnaseq <- GDCquery(
            project = c("TCGA-COAD","TCGA-READ"),
            data.category = "Transcriptome Profiling",
            data.type = "Gene Expression Quantification",
            workflow.type = "HTSeq - FPKM-UQ")

intersect(gsub("\\.","-",colnames(TCGA_COAD_protein)),substr(query.rnaseq$results[[1]]$cases,1,12)) %>% length()

## [1] 88