params {DMCFB} | R Documentation

## params

### Description

parameters name and their descriptions

### Arguments

`methReads` | The matrix `methReads` contains the number of methylated reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`totalReads` | The matrix `totalReads` contains the number of reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`methLevels` | The matrix `methLevels` contains the predicted methylation level spanning a CpG-site using Bayesian functional regression models. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`rowRanges` | A `GRanges` or `GRangesList` object describing the ranges of interest. Names, if present, become the row names of the `SummarizedExperiment` object. The length of the `GRanges` or `GRangesList` must equal the number of rows of the matrices in `assays`. If `rowRanges` is missing, a `SummarizedExperiment` instance is returned.
`colData` | Object of class `'DataFrame'` containing information on variable values of the samples
`metadata` | A `list` of storing MCMC samples or DMCs
`object` | A `BSDMC-class` object
`value` | An integer matrix
`name` | A character list
`obj1` | A `BSDMC-class`
`obj2` | A `BSDMC-class`
`files` | A character list
`file` | A character
`nCores` | An integer value specifying the number of machine cores for parallel computing
`mc.cores` | An integer greater than 0
`pSize` | An integer value specifying the number of cytosines in a regrion to be used in a Bayesian functiona regression model for DMC detection
`bwa` | An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the group-specific effects of the Bayesian functional regression model
`bwb` | An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the individual-specific effects of the Bayesian functional regression model
`nBurn` | An integer value specifying the number of burn-in samples
`nThin` | An integer value specifying the thining number in MCMC
`nMC` | An integer value specifying the number of MCMC samples after burn-in
`sdv` | An double value specifying the standard deviation of priors
`alpha` | A numeric value specifying the level of α in credible interval (1-α)\%
`col` | A character vector indicating which colors to alternate.
`sfiles` | A logical value indicating whether files to be saved or not.
`region` | An integer vector of length two specifying which subset of the object to be plotted
`nSplit` | A integer value specifying the number of subsets must be done for plotting the results of DMC identification
`parList` | A list specifying plots parameters, see `par`
`...` | other possible parameters

### Author(s)

Farhad Shokoohi <shokoohi@icloud.com>

[Package DMCFB version 1.6.0 Index]