Format scMethrix matrix to long form data for plotting

Source: R/scMethrix_plot.R

Format scMethrix matrix to long form data for plotting

prepare_plot_data(
  scm = NULL,
  assay = "score",
  regions = NULL,
  n_cpgs = 25000,
  pheno = NULL,
  verbose = TRUE,
  na.rm = T
)

Arguments

scm

scMethrix; the single cell methylation experiment
assay

string; name of an existing assay. Default = "score"
regions

Granges; genomic regions to be summarized. Could be a data.table with 3 columns (chr, start, end) or a GenomicRanges object
n_cpgs

integer; Use these many random CpGs for plotting. Default 25000. Set it to NULL to use all - which can be memory expensive. The seed will be set to n_cpgs for consistency.
pheno

string; Col name of colData(m). Will be used as a factor to color different groups
verbose

boolean; Flag for outputting function status messages. Default = TRUE
na.rm

boolean; remove NA values from the output

Value

'Long' matrix for methylation