clinical_terms: Search for clinical terms for all available tumors

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

Description

Search for clinical terms for all available tumors

Usage

clinical_terms(
  name,
  work_dir,
  tumor = "all",
  data_type,
  group_number = 2,
  term,
  data_base = "legacy",
  term_keyword = NULL,
  tumor_with_term = 1,
  p_cutoff = 0.05,
  fdr_cutoff = 0.05,
  confidence_level = 0.95,
  width = 7,
  height = 7,
  res = 300,
  unit = "in",
  image_format = "svg",
  env,
  cex_axix_x = 16,
  cex_axix_y = 16
)

Arguments

name	A character string indicating the desired values to be used in next analysis. For instance, "HIF3A" in the legacy gene expression matrix, "mir-1307" in the miRNA quantification matrix, or "HER2" in the protein quantification matrix.
work_dir	A character string specifying the path to work directory.
tumor	A character vector indicating which tumors should be used in the analysis. The default is "all".
data_type	A character string indicating which data_type will be used to group the patients. Only needed when the environment was not created yet and the user does not have the term argument.
group_number	Numerical value indicating how many groups should be generated. This argument is advisable if subcategory number is larger than 5. The default is 2.
term	A character string containing the clinical term to be used.
data_base	A character string specifying "GDC" for GDC Data Portal or "legacy" for GDC Legacy Archive.
term_keyword	A character string containing a possible fragment of the term. Used when the specific term is unknown.
tumor_with_term	A numerical value indicating the minimum number of tumors containing a specific term with the keyword used. The default is 1.
p_cutoff	Numerical value indicating the maximum value for p-values. The default is 0.05.
fdr_cutoff	Numerical value indicating the maximum value for FDR values. The default is 0.05.
confidence_level	A numerical value containing the confidence interval to be used. The default is 0.95.
width	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
height	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
res	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
unit	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
image_format	A character string indicating which image_format will be used. It could be "png" or "svg". The only unit available in "svg" is inches ('in'). The default is "png".
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).
cex_axix_x, cex_axix_y	A numerical value giving the amount by which labels in X and Y axis respectively should be modified relative to the default size. The default value is 16 for both arguments.

Value

the groups generated after using the seleted clinical category and store it inside the determined environment name.

Examples

library(DOAGDC)

for (tumor in c("CHOL", "UCS", "OV")) {
    download_gdc(
        data_type = "clinical",
        data_base = "gdc",
        work_dir = "~/Desktop",
        tumor = tumor
    )
}

# searching terms having the keyword inserted in common 'tumor_with_term = 3'
clinical_terms(
    tumor = c("CHOL", "UCS", "OV"),
    data_base = "gdc",
    term_keyword = "year",
    work_dir = "~/Desktop",
    tumor_with_term = 3
)

# searching all terms available with at least three tumors in common
clinical_terms(
    tumor = c("CHOL", "UCS", "OV"),
    term_keyword = "",
    data_base = "gdc",
    work_dir = "~/Desktop",
    tumor_with_term = 3
)

# using the analysis with a specified term

download_gdc(
        data_type = "gene",
        data_base = "gdc",
        htseq = "FPKM",
        work_dir = "~/Desktop",
        tumor = "CHOL")

concatenate_expression(
    name = "ENSG00000124440",
    data_type = "gene",
    data_base = "gdc",
    work_dir = "~/Desktop",
    htseq = "FPKM",
    tumor = "CHOL")

clinical_terms(
    "ENSG00000124440",
    "~/Desktop",
    "CHOL",
    "gene",
    data_base = "gdc",
    env = CHOL_GDC_gene_tumor_data,
    term = "gender")

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