BSDMCs-class: BSDMCs object

Description Arguments Value Slots Author(s) Examples

Description

The BSDMCs object is an S4 class that represents differentially methylated CpG sites (DMCs) in BS-Seq Data.

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.

methVars

The matrix methVars contains the variances of the corresponding methLevels obtianed from MCMC.

Value

A BSDMCs-class object

Slots

methReads

An integer matrix

totalReads

An integer matrix

methLevels

A numeric matrix

methStates

An integer matrix

methVars

A double matrix

Author(s)

Farhad Shokoohi <[email protected]>

Examples

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nr <- 500; nc <- 16
metht <- matrix(as.integer(runif(nr * nc, 0, nr)), nr)
methc <- matrix(rbinom(n=nr*nc,c(metht),prob = runif(nr*nc)),nr,nc)
meths <- matrix(as.integer(runif(nr * nc, 0, 10)), nr)
methl <- methc/metht
methv <- matrix((runif(nr * nc, 0.1, 0.5)), nr)
r1 <- GRanges(rep('chr1', nr), IRanges(1:nr, width=1), strand='*')
names(r1) <- 1:nr
cd1 <- DataFrame(Group=rep(c('G1','G2'),each=nc/2),row.names=LETTERS[1:nc])
OBJ2 <- cBSDMCs(rowRanges=r1,methReads=methc,totalReads=metht,
methLevels=methl,methStates=meths,methVars=methv,colData=cd1)
OBJ2

shokoohi/DMCHMM documentation built on Sept. 6, 2018, 1:55 p.m.