params: params

Description Arguments Author(s)

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.

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 numeric value

...

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.

Author(s)

Farhad Shokoohi <[email protected]>


shokoohi/DMCHMM documentation built on Sept. 1, 2017, 12:52 p.m.