readsData: An S4 class to represent summarised counts and the output of...

In denoiSeq: Differential Expression Analysis Using a Bottom-Up Model

Description

An S4 class to represent summarised counts and the output of Bayesian inference.

Slots

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.

denoiSeq documentation built on May 2, 2019, 9:33 a.m.