params: params

In shokoohi/DMCFB: Differentially Methylated Cytosines via a Bayesian Functional Approach

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 <[e-mail]>

shokoohi/DMCFB documentation built on April 21, 2022, 5:53 a.m.