coco: Interactive Cancer Explorer

devtools::load_all()

cohort_new(
  path = system.file("cohorts/example_TCGA_LAML", package = "coco"),
  name = "TCGA Acute Myeloid Leukemia (LAML) for examples utils",
  cancer_type = "LAML",
  data_provider = "TCGA",
  maintainer = "Shixiang Wang <wangsx1@sysucc.org.cn>",
  doi = NA,
  year = 2016,
  dataset_list = data.frame(
    id = c("example_TCGA_LAML_patient_info",
           "example_TCGA_LAML_gene_expr_HTSeq_count",
           "example_TCGA_LAML_MAF",
           "example_TCGA_LAML_somatic_CNV"),
    name = c("Patient information",
             "Gene expression in log2(count)",
             "Mutation list",
             "Copy number segment"),
    genome_build = c(NA, "hg19", "hg19", "hg19"),
    data_platform = c("Clinical", "RNA-Seq", "WES", "SNP-Array"),
    data_type = c("Phenotype", "Gene expression", "Mutation", "CNV"),
    data_format = c("PatientInfo", "Matrix", "MAF", "Segment"),
    tags = c("survival,FAB", "HTSeq", NA, NA)
  ), verbose = TRUE
)