getNegativeBinomialParameters: Get all parameters of the NB at once

In csoneson/compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Get all parameters of the NB at once

Description

Get both the mean and the dispersions of the NB as matrices for all indices.

Usage

getNegativeBinomialParameters(
  n.vars,
  S1,
  prob.S1,
  sum.S1,
  truedispersions.S1,
  nfact_length.S1,
  S2,
  prob.S2,
  sum.S2,
  truedispersions.S2,
  nfact_length.S2,
  seq.depths
)

Arguments

n.vars	The initial number of genes in the simulated data set. Based on the filtering conditions (filter.threshold.total and filter.threshold.mediancpm), the number of genes in the final data set may be lower than this number.
S1	Indices in condition 1.
prob.S1	Vector of means for condition 1.
sum.S1	Sum of means for condition 1.
truedispersions.S1	Vector of dispersions for condition 1.
nfact_length.S1	Matrix of length factors for condition 1.
S2	Indices in condition 2.
prob.S2	Vector of means for condition 2.
sum.S2	Sum of means for condition 2.
truedispersions.S2	Vector of dispersions for condition 2.
nfact_length.S2	Matrix of length factors for condition 2.

Value

A list of parameters for each entry of the count matrix:

count_means

a matrix of mean for each gene and sample.

count_dispersions

a matrix of dispersions for each gene and sample.

csoneson/compcodeR documentation built on Nov. 3, 2024, 6:05 a.m.