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: |
p.edge |
The used input parameter |