semseeker: Calculate stochastic epi mutations from a methylation dataset...

In drake69/semseeker: Stochastic Epigenetic Mutations SEM Seeker

Calculate stochastic epi mutations from a methylation dataset as outcome report of pivot

Description

Calculate stochastic epi mutations from a methylation dataset as outcome report of pivot

Usage

semseeker(
  sample_sheet,
  methylation_data,
  result_folder,
  bonferroni_threshold = 0.05,
  maxResources = 90,
  iqrTimes = 3,
  parallel_strategy = "multisession",
  ...
)

Arguments

sample_sheet	dataframe with at least a column Sample_ID to identify samples
methylation_data	matrix of methylation data
result_folder	where the result will be saved
bonferroni_threshold	= 0.05 #threshold to define which pValue adjusted to define an epilesion
maxResources	percentage of how many available cores will be used default 90 percent, rounded to the lowest integer
iqrTimes	how many times below the first quartile and over the third quartile the interqauartile is "added" to define the outlier
parallel_strategy	which strategy to use for parallel executio see future vignete: possibile values, none, multisession,sequential, multicore, cluster
...	other options to filter elaborations

Value

files into the result folder with pivot table and bedgraph.

drake69/semseeker documentation built on Sept. 17, 2023, 12:22 a.m.