birthMoveK1: Birth move in the case that only one nucleosome is present

Description Usage Arguments Value Author(s) Examples

View source: R/rjmcmcMethodsIntern.R

Description

Attempt to add a component for a new nucleosome in the case that only one nucleosome is present k = 1

Usage

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birthMoveK1(paramValues, kValue, muValue, sigmafValue, sigmarValue, deltaValue,
  wValue, dfValue, aValue, dimValue)

Arguments

paramValues

a list containing:

  • startPSF a vector of positive integer, the start position of all the forward reads.

  • startPSR a vector of positive integer, the start position of all the reverse reads.

  • kmax a integer the maximum number of nucleosomes allowed.

  • lambda a positive numeric, the theorical mean of the Poisson distribution.

  • minReads a integer, the minimum number of reads in a potential canditate region.

  • y a vector of numeric, the position of all reads ( including forward and reverse reads).

  • nr a integer, the number of reverse reads.

  • nf a integer, the number of forward reads.

  • nbrReads a integer, the total number of reads (including forward and reverse reads).

  • zeta integer, the length of a nucleosome.

  • deltamin a integer, the minimum distance between the maxima of the forward and reverse reads position densities for each nucleosome.

  • deltamax a integer, the maximum distance between the maxima of the forward and reverse reads position densities for each nucleosome.

  • minReadPos a numeric, the minimum position of the reads.

  • maxReadPos a numeric, the maximum position of the reads.

  • nbrIterations a integer, the number of iterations.

kValue

a integer, the number of nucleosomes.

muValue

a vector of numeric of length kValue, the positions of the nucleosomes.

sigmafValue

a vector of numeric of length kValue, the variance of the forward reads for each nucleosome.

sigmarValue

a vector of numeric of length kValue, the variance of the reverse reads for each nucleosome.

deltaValue

a vector of numeric of length kValue, the distance between the maxima of the forward and reverse reads position densities for each nucleosome.

wValue

a vector of positive numerical of length kValue, the weight for each nucleosome.

dfValue

a vector of positive numerical of length kValue, the degrees of freedom for each nucleosome.

aValue

a vector of positive numerical of length kValue + 1, the positions, on the chromosome, delimiting the regions of the reads associated with each nucleosome.

dimValue

a vector of positive numerical of length kValue, the number of reads associated to each nucleosome.

Value

a list containing:

Author(s)

Rawane Samb, Pascal Belleau, Astrid Deschenes

Examples

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## Load dataset
data(reads_demo)

## Create a list containing the mandatory parameters
paramList <- list(kmax = 30L, nf = length(reads_demo$readsForward),
nr = length(reads_demo$readsReverse),
nbrReads = length(reads_demo$readsForward) + length(reads_demo$readsReverse),
y = sort(c(reads_demo$readsForward, reads_demo$readsReverse)),
startPSF = reads_demo$readsForward,
startPSR = reads_demo$readsReverse, lambda = 2,
zeta = 147, deltamin = 142, deltamax = 152,
minReadPos = min(c(reads_demo$readsReverse, reads_demo$readsForward)),
maxReadPos = max(c(reads_demo$readsReverse, reads_demo$readsForward)))

## Create a list containing the mandatory parameters
RJMCMC:::birthMoveK1(paramValues = paramList, kValue = 1L,
muValue = c(73008.53, rep(0, 29)), sigmafValue = c(1, rep(0, 29)),
sigmarValue = c(1, rep(0 ,29)),
deltaValue = c(61.03185, rep(0, 29)), wValue = c(1, rep(0, 29)),
dfValue = c(3, rep(0, 29)),
aValue = c(min(c(reads_demo$readsReverse, reads_demo$readsForward)),
max(c(reads_demo$readsReverse, reads_demo$readsForward)), rep(0, 29)),
dimValue = c(length(reads_demo$readsForward) +
length(reads_demo$readsReverse), rep(0, 29)))

ArnaudDroitLab/RJMCMC documentation built on Sept. 13, 2017, 5:48 a.m.