Writes bedGraphs from methrix object

write_bedgraphs(
  m,
  output_dir = NULL,
  rm_NA = TRUE,
  force = FALSE,
  n_thr = 4,
  compress = TRUE,
  SeqStyle = "UCSC",
  multiBed = NULL,
  metilene = FALSE,
  phenoCol = NULL
)

Arguments

m	`methrix` object
output_dir	Output directory name where the files should be saved. If `NULL` creats a `tempdir`
rm_NA	remove NAs
force	forces to create files if they are existing
n_thr	Default 4.
compress	Whether to compress the output. Default TRUE
SeqStyle	Default `UCSC` with `chr` prefix.
multiBed	Default NULL. If provided a filename, a single bedGraph file with all samples included is generated.
metilene	Default FALSE. If TRUE outputs bedgraphs in `metilene` format that can be directly used for DMR calling with `metilene`. This option works only when `multiBed = TRUE`.
phenoCol	Default NULL. `condition` column from colData. Only applicable if `metilene = TRUE`

Value

writes bedgraph files to output

Examples

data('methrix_data')
write_bedgraphs(m = methrix_data, output_dir = './temp')
#> ----------------------
#> *Writing bedGraphs:
#> **Writing C1
#> **Writing C2
#> **Writing N1
#> **Writing N2
#> ----------------------
#Export to metline format for DMR calling with metline
write_bedgraphs(m = methrix_data, output_dir = "./temp", rm_NA = FALSE, metilene = TRUE,multiBed = "metline_ip", phenoCol = "Condition")
#> ----------------------
#> *Writing ./temp/metline_ip.bedGraph.gz 
#> ----------------------