rjmcmcNucleo {RJMCMCNucleosomes} | R Documentation |
Function that calls the core of the nucleosome positioning mapping function that is implemented in C++.
rjmcmcNucleo(startPosForwardReads, startPosReverseReads, nbrIterations, kMax, lambda, minInterval, maxInterval, minReads = 5L, adaptIterationsToReads = TRUE, vSeed = -1)
startPosForwardReads |
a |
startPosReverseReads |
a |
nbrIterations |
a positive |
kMax |
a positive |
lambda |
a positive |
minInterval |
a |
maxInterval |
a |
minReads |
a positive |
adaptIterationsToReads |
a |
vSeed |
a |
a list
containing:
k a integer
, the number of nucleosomes.
k_max a integer
, the maximum number of nucleosomes
obtained during the iteration process.
it a vector
of integer
of length
k
, the variance of the forward reads for each nucleosome.
nbState a integer
, the number of changes of state.
mu a matrix
of numeric
with k_max
columns
and nbState
row containing, in each row, the mu
values
associated the the state identified by the row number.
muHat a matrix
of numeric
with k_max
columns
and k_max
rows containing, in each row, the mean mu
values
associated the number of nucleosomes detected. The row number
corresponds to the number of nucleosomes detected.
nbK a vector
of length k_max
containing
integer
, the number of iterations
which detected a specific number of nucleosomes. The position in the vector
correspond to the number of nucleosomes.
Pascal Belleau, Astrid Deschenes
data(reads_demo_01) forward <- start(reads_demo_01[strand(reads_demo_01) == "+"]) reverse <- end(reads_demo_01[strand(reads_demo_01) == "-"]) ## Run nucleosome positioning result <- RJMCMCNucleosomes:::rjmcmcNucleo( startPosForwardReads = forward, startPosReverseReads = reverse, nbrIterations = 1000, lambda = 2, kMax = 30, minInterval = 146, maxInterval = 292, minReads = 5, adaptIterationsToReads = TRUE, vSeed = -1) ## Print the final estimation of the number of nucleosomes result$k ## Print the position of nucleosomes result$mu