R: Calculate expression ratio distribution

get_ratio_distribution {Corbi} | R Documentation

## Calculate expression ratio distribution

### Description

Calculate the lower and upper quantiles of expression ratios for each pair of genes, and estimate the parameters of negative binomial distribution from reference expression data.

### Usage

    get_ratio_distribution(
      ref.expr.matrix,
      p.edge = 0.1,
      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.
`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 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`.

[Package Corbi version 0.6-1 Index]