params: params
In shokoohi/DMCHMM: Differentially Methylated CpG using Hidden Markov Model

params

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 Hidden Markov model. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`methVars`	The matrix `methVars` contains the variances of the corresponding `methLevels` obtianed from MCMC.
`methStates`	The matrix `methStates` contains the state of methylation obtained from Hidden Markov model spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`. The value of state is stored in `metadata`, named `Beta`.
`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`	An optional `list` of arbitrary content describing the overall experiment
`object`	A `BSData-class` or `BSDMCs-class` object
`value`	An integer matrix
`obj1`	A `BSData-class` or `BSDMCs-class`
`obj2`	A `BSData-class` or `BSDMCs-class`
`files`	A character list
`file`	A character
`name`	A character list
`MaxK`	An integer value
`MaxEmiter`	An integer value
`epsEM`	A positive numeric value
`useweight`	A logical value
`mc.cores`	An integer greater than 0
`nburn`	An integer value
`nthin`	An integer value
`nsamp`	An integer value
`formula`	A formula
`FDRthreshold`	A numeric value
`Methylthreshold`	A positive numeric value; the default is 0.001
`weightfunction`	A function to create weights using variance obtained form the MCMC algorithm
`...`	other possible parameters
`col`	A character vector indicating which colors to alternate.
`chrlabs`	A character vector equal to the number of chromosomes specifying the chromosome labels (e.g., `c(1:22, "X", "Y", "MT")`).
`suggestiveline`	Where to draw a "suggestive" line. Default -log10(1e-5). Set to FALSE to disable.
`genomewideline`	Where to draw a "genome-wide sigificant" line. Default -log10(5e-8). Set to FALSE to disable.
`highlight`	A character vector of SNPs in your dataset to highlight. These SNPs should all be in your dataset.
`logp`	If TRUE, the -log10 of the p-value is plotted. It isn't very useful to plot raw p-values, but plotting the raw value could be useful for other genome-wide plots, for example, peak heights, bayes factors, test statistics, other "scores," etc.
`annotatePval`	If set, SNPs below this p-value will be annotated on the plot.
`annotateTop`	If TRUE, only annotates the top hit on each chromosome that is below the annotatePval threshold.
`windowsize`	An integer value for partitioning data into windows of size windowsize.