BuildSubnetwork | R Documentation |
Find the subnetwork of significant edges connecting the genes.
BuildSubnetwork(
geneSet,
networks,
alpha,
hopConstraint,
nullDistribution,
verbose = FALSE,
topX = NULL,
doFDRAdjustment = TRUE,
pValueChunks = 100,
loadPValues = FALSE,
pValueFile = "pvalues.RDS"
)
geneSet |
A character vector of genes comprising the targets of interest. |
networks |
A list of bipartite (PANDA-like) networks, where each network is a data frame with the following format: tf,gene,score |
alpha |
The significance cutoff for the statistical test. |
hopConstraint |
The maximum number of hops to be considered between gene pairs. Must be an even number. |
nullDistribution |
The null distribution, specified as a vector of values. |
verbose |
Whether or not to print detailed information about the run. |
topX |
Select the X lowest significant p-values for each gene. NULL by default. |
doFDRAdjustment |
Whether or not to perform FDR adjustment. |
pValueChunks |
The number of chunks to split when calculating the p-value. This parameter allows the edges to be split into chunks to prevent memory errors. |
loadPValues |
Whether p-values should be loaded from pValueFile or re-generated. Default is FALSE. |
pValueFile |
The file where the p-values should be saved. If NULL, they are not saved and need to be recalculated. |
A bipartite subnetwork in the same format as the original networks.
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