readsData {denoiSeq} | R Documentation |
An S4 class to represent summarised counts and the output of Bayesian inference.
counts
A positive integer matrix containing summarised counts for each genomic event (genes, exons, transcripts, etc) in the two conditions, A and B.
replicates
A list containing the indices of the columns that belong to
each of the two experimental conditions, A and B. It is defaulted to A =
1:(n/2), B = (n/2+1):n for an m
by n
matrix.
geneNames
A character vector containing the names of the genomic event. It is appropriately defaulted to names of the matrix.
initValues
A list containing initial values for each parameter.
Defaulted to N_A
= rep(1, nrow(counts)), N_B
= rep(1,
nrow(counts)), p
= 0.0001, f
= 0.01.
stepSizes
A list containing step sizes for sampling each parameter.
Defaulted to stepsizeN_A
= rep(1, nrow(counts)), stepsizeN_B
=
rep(1, nrow(counts)), stepsize_p
= 1e3, stepsize_f
= 5e7
output
A list containing the samples for each parameter which are generated by Bayesian inference. It can only be filled inside the results function.