get_ratio_distribution2 {Corbi}

Calculate expression ratio distribution

Description

Calculate the lower and upper quantiles of expression ratios after trimming the extreme values, and estimate the parameters of negative binomial distribution from reference expression data.

Usage

get_ratio_distribution2(
  ref.expr.matrix,
  p.edge = 0.1,
  p.trim = 0.3,
  log.expr = FALSE,
  scale.degree = FALSE,
  use.parallel = FALSE
)

Arguments

ref.expr.matrix

The reference expression matrix. Each row represents a gene and each column represents a sample.

p.edge

The expected probability of edges in the expression ratio network for a normal sample.

p.trim

The percentage of lower or upper extreme values to be trimmed from the expression ratios for each pair of genes.

log.expr

Logical variable indicating whether the input expression matrix is in logarithmic scale.

scale.degree

Logical variable indicating whether the degree values are scaled according to the dropout rate.

use.parallel

Logical variable indicating to use the BiocParallel package to accelerate computation.

Value

This function will return a list with the following components:

LB

A numeric matrix with element [i,j] represents the lower quantile of trimmed expressioin ratios for gene pairs (i, j).

NB

A numeric vector with two elements: size and mu, which are the estimated parameters of negative binomial distribution.

p.edge

The used input parameter p.edge.

p.trim

The used input parameter p.trim.