Extract pattern data

Extract pattern data

gpatterns.extract(..., intervals, colnames = NULL, elements = c("fid",
  "ncpg", "n", "n0", "n1", "nx", "nc", "pat_meth"), add_bipolar_stats = FALSE,
  add_patterns = FALSE, add_cpg_content = FALSE, cpg_nhood = 500,
  add_coordinates = TRUE, tidy = TRUE, dsn = NULL, na.rm = TRUE)

Arguments

...

tracks to extract

intervals

genomic scope to extract from intervals

colnames

names for the tracks

elements

elements to extract. default: fid,ncpg,n,n0,n1,nx,nc,pat_meth

add_bipolar_stats

add stats from bipolar model (if computed)

add_patterns

add patterns

add_cpg_content

add centered cpg content

cpg_nhood

scope for centered cpg content (in bp)

add_coordinates

add chrom,start,end for fragments

tidy

return tidy output

dsn

extract downsampled data

na.rm

remove rows with missing data