Prepare methylation and expression data of a gene in TCGA tumors

Creates a Dataframe giving for each TCGA sample, the methylation level of a gene (mean methylation of probes located in its promoter) and the expression level of the gene (TPM value).

Usage

prepare_TCGA_methylation_expression(
  tumor = "all",
  gene = NULL,
  nt_up = NULL,
  nt_down = NULL,
  include_normal_tissues = FALSE
)

Arguments

tumor

character defining the TCGA tumor type. Can be one of "SKCM", "LUAD", "LUSC", "COAD", "ESCA", "BRCA", "HNSC", or "all" (default).

gene

character selected CT gene.

nt_up

numeric(1) indicating the number of nucleotides upstream the TSS to define the promoter region (1000 by default)

nt_down

numeric(1) indicating the number of nucleotides downstream the TSS to define the promoter region (200 by default)

include_normal_tissues

logical(1). If TRUE, the function will include normal peritumoral tissues in addition to tumoral samples. Default is FALSE.

Value

a Dataframe giving for each TCGA sample, the methylation level of a gene (mean methylation of probes located in its promoter) and the expression level of the gene (TPM value). The number of probes used to estimate the methylation level is also reported.

Examples

if (FALSE) { # \dontrun{
  CTexploreR:::prepare_TCGA_methylation_expression("LUAD", gene = "TDRD1")
} # }