MMRF-COMMPASS

1 MMRF-COMMPASS

library(dplyr)
library(TCGAbiolinks)
library(SummarizedExperiment)

query <- GDCquery(
    project = "MMRF-COMMPASS",
    data.category = "Transcriptome Profiling", 
    data.type = "Gene Expression Quantification",
    workflow.type = "HTSeq - Counts"
)

GDCdownload(query,files.per.chunk = 100)
data <- GDCprepare(query)

data

## class: RangedSummarizedExperiment 
## dim: 56512 859 
## metadata(1): data_release
## assays(1): HTSeq - Counts
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(859): MMRF_2475_1_BM_CD138pos MMRF_2836_1_BM_CD138pos ...
##   MMRF_2794_1_BM_CD138pos MMRF_2570_1_BM_CD138pos
## colData names(41): barcode sample ... project_id name

rowRanges(data)

## GRanges object with 56512 ranges and 3 metadata columns:
##                   seqnames              ranges strand | ensembl_gene_id
##                      <Rle>           <IRanges>  <Rle> |     <character>
##   ENSG00000000003     chrX 100627108-100639991      - | ENSG00000000003
##   ENSG00000000005     chrX 100584936-100599885      + | ENSG00000000005
##   ENSG00000000419    chr20   50934867-50958555      - | ENSG00000000419
##   ENSG00000000457     chr1 169849631-169894267      - | ENSG00000000457
##   ENSG00000000460     chr1 169662007-169854080      + | ENSG00000000460
##               ...      ...                 ...    ... .             ...
##   ENSG00000281904     chr2   90365737-90367699      + | ENSG00000281904
##   ENSG00000281909    chr15   22480439-22484840      - | ENSG00000281909
##   ENSG00000281910    chr16   58559796-58559931      - | ENSG00000281910
##   ENSG00000281912     chr1   45303910-45305619      + | ENSG00000281912
##   ENSG00000281920     chr2   65623272-65628424      + | ENSG00000281920
##                   external_gene_name original_ensembl_gene_id
##                          <character>              <character>
##   ENSG00000000003             TSPAN6       ENSG00000000003.13
##   ENSG00000000005               TNMD        ENSG00000000005.5
##   ENSG00000000419               DPM1       ENSG00000000419.11
##   ENSG00000000457              SCYL3       ENSG00000000457.12
##   ENSG00000000460           C1orf112       ENSG00000000460.15
##               ...                ...                      ...
##   ENSG00000281904         AC233263.6        ENSG00000281904.1
##   ENSG00000281909            HERC2P7        ENSG00000281909.1
##   ENSG00000281910           SNORA50A        ENSG00000281910.1
##   ENSG00000281912          LINC01144        ENSG00000281912.1
##   ENSG00000281920         AC007389.5        ENSG00000281920.1
##   -------
##   seqinfo: 24 sequences from an unspecified genome; no seqlengths

colData(data) %>%
    as.data.frame() %>%
  DT::datatable(filter = 'top',
                style = "bootstrap",
                extensions = 'Buttons',
                options = list(scrollX = TRUE, 
                               dom = 'Bfrtip',
                               buttons = I('colvis'),
                               keys = TRUE, 
                               pageLength = 10), 
                rownames = FALSE,
                caption = "meta-analysis results")

## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.html

colData(data) %>% as.data.frame %>% plyr::count(vars = "sample_type")