R/constants.R

In ShixiangWang/coco: Interactive Cancer Explorer

# data to export ------------------

#' The specification to determine how to generate row index file for specified data format
#' @export
SPEC_ROWINDEX = list(
    Segment = "Sample",
    MAF = c("Tumor_Sample_Barcode", "Hugo_Symbol"),
    Matrix = ".c1", # .c1 represents column 1
    PatientInfo = "patient",
    SampleInfo = "sample"
)

#' The specification to determine how to count sample number in a dataset
#' @export
SPEC_SAMPINDEX = list(
    Segment = "Sample",
    MAF = "Tumor_Sample_Barcode",
    Matrix = "ncol-1",
    PatientInfo = "patient",
    SampleInfo = "sample"
)

#' Valid options for datasets
#' @export
SPEC_DATASET_OPTIONS = list(
    platforms = c("Clinical", "WES", "WGS", "Target Sequencing", "RNA-Seq", "SNP-Array"),
    types = c("CNV", "Mutation", "Gene expression", "DNA methylation", "Phenotype"),
    formats = c("Segment", "MAF", "Matrix", "PatientInfo", "SampleInfo")
)

# data not to export ----------------