Promoter methylation of any gene in fetal germ cells — fetal_germcells_mean

Plots a heatmap of mean promoter methylation levels of any genes in fetal germ cells, using WGSB data from "Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution" (Li et al. 2021). Methylation levels in tissues correspond to the mean methylation of CpGs located in range of 1000 pb upstream and 500 pb downstream from gene TSS.

Usage

fetal_germcells_mean_methylation(
  genes = NULL,
  include_CTP = FALSE,
  values_only = FALSE
)

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.

Value

Heatmap of mean promoter methylation of any gene in normal tissues. If values_only = TRUE, a SummarizeExperiment with methylation values is returned instead.

Examples

fetal_germcells_mean_methylation()
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache
#> Warning: 2 out of 146 names invalid: FAM230C, FLJ36000.
#> See the manual page for valid types.

fetal_germcells_mean_methylation(c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEC2"))
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache