netDEG {Corbi} | R Documentation |
Perform netDEG for two group samples.
netDEG( ref.expr.matrix, expr.matrix, p.edge = 0.1, summarize = c("gene", "sample"), summarize.method = c("sumlog", "sumlog"), summarize.shrink = c(Inf, Inf), log.expr = FALSE, zero.as.dropout = TRUE, scale.degree = TRUE, use.parallel = FALSE )
ref.expr.matrix |
The reference expression matrix. Each row represents a gene and each column represents a sample. |
expr.matrix |
The test 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. |
summarize |
Character vector indicating how to summarize the results. Available methods are |
summarize.method |
Character vector indicating the methods used to summarize the results. See |
summarize.shrink |
Numeric vector indicating the shrink parameter to summarize the results. See |
log.expr |
Logical variable indicating whether the input expression matrix is in logarithmic scale. |
zero.as.dropout |
Logical variable indicating whether the zero expressions are regarded as dropouts. |
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:
up |
A numeric matrix with same dimension as |
down |
A numeric matrix with same dimension as |
twoside |
A numeric matrix with same dimension as |
rev |
A list containing the reverse comparison results, containing three components: |
gene |
A list containing the gene-wise summaried results, containing three components: |
sample |
A list containing the sample-wise summaried results, containing three components: |