methyl_master_formatting_sesame: methyl_master_formatting_sesame

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

methyl_master_formatting_sesame

Description

formatting the results of the sesame functionality to prepare for comparison and output

Usage

methyl_master_formatting_sesame(
  sesame.form.seg = NULL,
  sesame.form.output.dir = getwd(),
  sesame.form.sample.sheet.path = NULL,
  sesame.form.reference = NULL,
  sesame.form.split.by = NULL,
  sesame.form.comparison = NULL,
  sesame.form.save.seg = FALSE,
  sesame.form.plot.individual = FALSE,
  sesame.form.thresholds = NULL,
  ...
)

Arguments

sesame.form.seg	The input sesame segmentation list for formatting
sesame.form.output.dir	The output dir for sesame formatting
sesame.form.reference	The sesame reference used in the analysis
sesame.form.split.by	The split.by field used in the sesame routine in the MethylMaster sample sheet
sesame.form.comparison	The MethylMaster comparison vector used in the Sesame routine analysis
sesame.form.save.seg	Whether or not to save the formatted seg output
sesame.form.plot.individual	Whether to plot the individual sesame sample signal plots
sesame.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 to pass to methyl_master_formatting_sesame
sample.form.sample.sheet.path	The path to the MethylMaster sample sheet

Value

Formatted seg list object for visualizing etc.

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