beta2m_values: Convert beta values to mvalues

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

Description

Convert beta values to mvalues

Usage

beta2m_values(probe_name, env, save_data = FALSE)

Arguments

probe_name	A character string containing the probe name desired from the selected 'name' probes.
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).
save_data	Logical value where TRUE indicates that the concatenate and filtered matrix should be saved in local storage. The default is FALSE.

Value

the beta values converted in mValues stored inside the determined environment name.

Examples

library(DOAGDC)

download_gdc(
   data_type = "methylation",
   data_base = "legacy", work_dir = "~/Desktop", tumor = "CHOL",
   platform = "Illumina Human Methylation 450"
)

concatenate_methylation(
    name = "HIF3A",
    data_base = "legacy",
    platform = "Illumina Human Methylation 450",
    tumor = "CHOL",
    work_dir = "~/Desktop"
)

beta2m_values(
   probe_name = "cg16672562",
   save_data = TRUE,
   env = CHOL_LEGACY_methylation_tumor_data
)

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