methyl_master_olaps_and_visualize: methyl_master_olaps_and_visualize

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

methyl_master_olaps_and_visualize

Description

perform overlaps analysis and visualization for the various routines.

Usage

methyl_master_olaps_and_visualize(
  ov.seg = NULL,
  ov.name = NULL,
  ov.output.dir = getwd(),
  ov.routine = NULL,
  ov.split.field = NULL,
  ov.keep.extra.columns = TRUE,
  ov.overlap.density = 0.1,
  ov.estimate.recurrence = FALSE,
  ov.simplify.reduce = weightedmean,
  ov.less.stringent.ra.setting = FALSE,
  ov.pvalue = 0.05,
  ov.plot.individual = FALSE,
  ...
)

Arguments

ov.seg	The formatted seg input object
ov.name	The name of the formatted seg input object
ov.output.dir	The output directory for the overlaps and visualization results
ov.routine	The specific routine that was run to produce the results
ov.split.field	The split.by field specified earlier in the analysis from the Sample Sheet
ov.keep.extra.columns	Keep the extra metadata columns in the output
ov.overlap.density	The populationRanges desnity value to use when caluclating overlaping CNV regions
ov.estimate.recurrence	Whether or not to use esitmate recursion (generates a p-value) for the overlaps regions identified by populationRanges
ov.simplify.reduce	The reduction function used to reduce the overlaps results
ov.less.stringent.ra.setting	Whether or not to use the more or less stringent overlaps filltering (ra denotes "Ragged Experiment" object)
ov.pvalue	The incoming CNV call p-value threshold to filter by before any overlaps caluclations are performed
ov.plot.individual	Whether to plot individual plots for the the sesame routine
...	Additional parameters to pass to methyl_master_olaps_and_visualize

Value

Output overlaps regions .CSVs and images

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