get_ratio_distribution | R Documentation |
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.
get_ratio_distribution( ref.expr.matrix, p.edge = 0.1, log.expr = FALSE, scale.degree = FALSE, use.parallel = FALSE )
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. |
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 |
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