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.
get_ratio_distribution2(
ref.expr.matrix,
p.edge = 0.1,
p.trim = 0.3,
log.expr = FALSE,
scale.degree = FALSE,
use.parallel = FALSE
)The reference expression matrix. Each row represents a gene and each column represents a sample.
The expected probability of edges in the expression ratio network for a normal sample.
The percentage of lower or upper extreme values to be trimmed from the expression ratios for each pair of genes.
Logical variable indicating whether the input expression matrix is in logarithmic scale.
Logical variable indicating whether the degree values are scaled according to the dropout rate.
Logical variable indicating to use the BiocParallel package to accelerate computation.
This function will return a list with the following components:
A numeric matrix with element [i,j] represents the lower quantile of trimmed expressioin ratios for gene pairs (i, j).
A numeric vector with two elements: size and mu,
which are the estimated parameters of negative binomial distribution.
The used input parameter p.edge.
The used input parameter p.trim.