filter_ceRNA_network: prepare ceRNA network and network centralities from SPONGE /...

In biomedbigdata/SPONGE: Sparse Partial Correlations On Gene Expression

prepare ceRNA network and network centralities from SPONGE / SPONGEdb for spongEffects

Description

prepare ceRNA network and network centralities from SPONGE / SPONGEdb for spongEffects

Usage

filter_ceRNA_network(
  sponge_effects,
  Node_Centrality = NA,
  add_weighted_centrality = T,
  mscor.threshold = NA,
  padj.threshold = NA
)

Arguments

sponge_effects	the ceRNA network downloaded as R object from SPONGEdb (Hoffmann et al., 2021) or created by SPONGE (List et al., 2019) (ends with _sponge_results in the SPONGE vignette)
Node_Centrality	the network analysis downloaded as R object from SPONGEdb (Hoffmann et al., 2021) or created by SPONGE and containing centrality measures. (List et al., 2019) (ends with _networkAnalysis in the SPONGE vignette, you can also use your own network centrality measurements) if network_analysis is NA then the function only filters the ceRNA network, otherwise it will filter the given network centralities, but will not recalculate them based on the filtered ceRNA network.
add_weighted_centrality	calculate and add weighted centrality measures to previously available centralities. Default = T
mscor.threshold	mscor threshold to be filtered (default: NA)
padj.threshold	adjusted p-value to be filtered (default: NA)

Value

list of filtered ceRNA network and network centrailies. You can access it with list$objectname for further spongEffects steps

biomedbigdata/SPONGE documentation built on Feb. 6, 2023, 10:19 p.m.