Builds network knowledge required by NicheNet. For this it calls a multitude of methods to download and combine data from various databases according to the settings. The content of the prior knowledge data is highly customizable, see the documentation of the related functions.
Arguments
- signaling_network
A list of parameters for building the signaling network, passed to
nichenet_signaling_network- lr_network
A list of parameters for building the ligand-receptor network, passed to
nichenet_lr_network- gr_network
A list of parameters for building the gene regulatory network, passed to
nichenet_gr_network- only_omnipath
Logical: a shortcut to use only OmniPath as network resource.
- small
Logical: build a small network for testing purposes, using only OmniPath data. It is also a high quality network, it is reasonable to try the analysis with this small network.
- tiny
Logical: build an even smaller network for testing purposes. As this involves random subsetting, it's not recommended to use this network for analysis.
- quality_filter_param
Arguments for
filter_intercell_network(quality filtering of the OmniPath ligand-receptor network). It is recommended to check these parameters and apply some quality filtering. The defaults already ensure certain filtering, but you might want more relaxed or stringent options.
Value
A named list with three network data frames (tibbles): the signaling, the ligand-receptor (lr) and the gene regulatory (gr) networks.
Examples
if (FALSE) {
networks <- nichenet_networks()
dplyr::sample_n(networks$gr_network, 10)
# # A tibble: 10 x 4
# from to source database
# <chr> <chr> <chr> <chr>
# 1 MAX ALG3 harmonizome_ENCODE harmonizome
# 2 MAX IMPDH1 harmonizome_ENCODE harmonizome
# 3 SMAD5 LCP1 Remap_5 Remap
# 4 HNF4A TNFRSF19 harmonizome_CHEA harmonizome
# 5 SMC3 FAP harmonizome_ENCODE harmonizome
# 6 E2F6 HIST1H1B harmonizome_ENCODE harmonizome
# 7 TFAP2C MAT2B harmonizome_ENCODE harmonizome
# 8 USF1 TBX4 harmonizome_TRANSFAC harmonizome
# 9 MIR133B FETUB harmonizome_TRANSFAC harmonizome
# 10 SP4 HNRNPH2 harmonizome_ENCODE harmonizome
}
# use only OmniPath:
omnipath_networks <- nichenet_networks(only_omnipath = TRUE)