write_bedgraphs: Writes bedGraphs from methrix object

In CompEpigen/methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Writes bedGraphs from methrix object

Description

Writes bedGraphs from methrix object

Usage

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

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
add_coverage	Should the output file contain information on coverage? Default FALSE

Value

writes bedgraph files to output

Examples

data('methrix_data')
write_bedgraphs(m = methrix_data, output_dir = './temp')
#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")

CompEpigen/methrix documentation built on July 24, 2024, 5:49 p.m.