methyl_master_formatting_champ: methyl_master_formatting_champ

In mmariani123/MethylMasteR: What the Package Does (One Line, Title Case)

methyl_master_formatting_champ

Description

formatting the champ seg results for overlaps and visualization etc.a Michael Mariani PhD Dartmouth College 2021

Usage

methyl_master_formatting_champ(
  champ.form.seg = NULL,
  champ.form.output.dir = getwd(),
  champ.form.save.seg = FALSE,
  champ.form.comparison = NULL,
  champ.form.padj = NULL,
  champ.form.thresholds
)

Arguments

champ.form.seg	The input ChAMP CNV segmentation results
champ.form.output.dir	The output directory used
champ.form.save.seg	Whether to save the formatted ChAMP results
champ.form.comparison	The MethylMaster comparison vector
champ.form.padj	The padj that was used in the ChAMP routine
champ.form.thresholds	The thresholds used to determine the CNV state, if NULL, the equation seg.state <- round(2^seg.means * 2) is used
...	Additional parameters passed to methyl_master_champ_formatting

Value

Formatted champ result as MethylMaster seg object for downstream analysis

mmariani123/MethylMasteR documentation built on June 22, 2022, 3:06 p.m.