Calculate Stochastic Epigenetic Mutations from a Methylation Dataset

Source: R/semseeker.R

The `semseeker` function processes a methylation dataset to identify stochastic epigenetic mutations and generates output reports. This involves working with sample sheets and signal data to produce pivot tables and bedgraph files.

semseeker(sample_sheet, signal_data, result_folder, ...)

Arguments

sample_sheet

A data frame containing at least a column named `Sample_ID` to identify samples. This can be a single data frame or a list of data frames.

signal_data

A matrix of methylation data. This can be a single data frame or a list of data frames.

result_folder

A string specifying the directory where the results will be saved.

...

Additional arguments for further processing options, including: - `parallel_strategy`: Strategy for parallel execution. Possible values are `none`, `multisession`, `sequential`, `multicore`, and `cluster`. - `maxResources`: Percentage of available cores to be used, default is 90 percent, rounded to the lowest integer. - `signal_intrasample`: A logical value indicating whether the signal data is intrasample. Default is `FALSE`. - `sliding_window_size`: An integer specifying the size of the sliding window. Default is 11. - `alpha`: A numeric value specifying the alpha threshold for the analysis. Default is 0.05. - `showprogress`: A logical value indicating whether to show a progress bar. Default is `TRUE`. - `iqrTimes`: A numeric value specifying the interquartile range multiplier to identify aberration in the data. Default is 3. - `sex_chromosome_remove`: A logical value indicating whether to remove the sex chromosomes. Default is `TRUE`. - `plot_format`: A string specifying the plot format. Default is "png". - `verbosity`: A numeric value specifying the verbosity level. Default is 0. - `marker`: A vector of string specifying the marker to be used for the analysis. Default are "MUTATIONS", "LESIONS","DELTARQ","DELTAQ","DELTAS","DELTAR","MEAN","DELTARP","DELTAP" - `areas`: A vector of string specifying the areas to be used for the analysis. Default are "GENE","CHR","ISLAND","PROBE"

Value

The function writes multiple files to the specified `result_folder`, including the processed sample sheet and result files in CSV format, along with pivot tables and bedgraph files.