Promoter methylation of any gene in normal tissues — normal_tissues_mean

Plots a heatmap of mean promoter methylation levels of any genes in normal tissues. Methylation levels in tissues correspond to the mean methylation of CpGs located in range of 1000 pb upstream and 200 pb downstream from gene TSS.

Usage

normal_tissues_mean_methylation(
  genes = NULL,
  include_CTP = FALSE,
  values_only = FALSE,
  na.omit = TRUE
)

Arguments

genes: character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP: logical(1) If TRUE, CTP genes are included. (FALSE by default).
values_only: logical(1), FALSE by default. If TRUE, the function will return the methylation values in all samples instead of the heatmap.
na.omit: logical(1) specifying if genes with missing methylation values in some tissues should be removed (TRUE by default). Note that no gene clustering will be done when methylation values are missing.

Value

Heatmap of mean promoter methylation of any gene in normal tissues. If values_only = TRUE, methylation values are returned instead.

Examples

normal_tissues_mean_methylation()
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache

normal_tissues_mean_methylation(c("MAGEA1", "MAGEA2", "MAGEA3", "MAGEA4"))
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache

normal_tissues_mean_methylation(c("MAGEA1", "MAGEA2", "MAGEA3", "MAGEA4"),
    na.omit = FALSE)
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache