table2_doagdc: From global to DOAGDC environment

In Facottons/DOAGDC: A Package to Download, Organize and Analyze Genomic Data Commons (GDC) Data

Description

From global to DOAGDC environment

Usage

table2_doagdc(
  table,
  data_type,
  normalization = TRUE,
  data_base,
  tumor,
  tumor_data = TRUE,
  env
)

Arguments

table	A matrix or data frame with data used in this package (i.e Gene, isoform and protein expression, methylation and mutation data)
data_type	Type of data. It could be "methylation", "mutation", "clinical_supplement", "biospecimen", "gene", or "clinical"(biotab). Only present in "Legacy" database:"protein", "Exon quantification", "miRNA gene quantification", "miRNA isoform quantification", "isoform", and "image". Only present in "GDC" database:"miRNA Expression Quantification", and "Isoform Expression Quantification" (miRNA).
normalization	Logical value where TRUE specify the desire to work with normalized files only. When FALSE, in the second run, do not forget to set env argument. This argument is only applyable to gene and isoform expression data from GDC Legacy Archive. The default is TRUE.
data_base	If the data was downloaded from GDC/Legacy data base, however not using DOAGDC, please specified which data base. If the data do not come from GDC/Legacy data base, and it is related with genome version GRCh 37, please insert "legacy" in this argument. Otherwise, if it is related with genome version GRCh 38, please insert "GDC" in this argument.
tumor	A character string contaning one of the 33 tumors available in the TCGA project. For instance, the "BRCA" stands for breast cancer.
tumor_data	Logical value where TRUE specifies the desire to work with tumor tissue files only. When set to FALSE, it creates two matrices, one containing tumor data and other containing data from not-tumor tissue. The default is TRUE.
env	A character string containing the environment name that should be used. If none has been set yet, the function will create one in global environment following the standard criteria: 'tumor_data_base_data_type_tumor_data' or 'tumor_data_base_data_type_both_data' (for tumor and not tumor data in separated matrices).

Value

the objects imported are stored inside the determined environment name.

Examples

patient <- paste0(paste0("patient_", LETTERS[1:4]))
genes <- paste0("gene_", seq(1, 5))
# generate a simulated gene expression matrix
example_gene_table <- matrix(
   runif(20, 0.0, 90.5), 5, 4, TRUE,
   list(genes, patient)
)
# without env created
table2_doagdc(example_gene_table,
   data_type = "gene",
   data_base = "legacy",
   tumor = "UCS"
)

Facottons/DOAGDC documentation built on April 7, 2020, 3:17 a.m.