View source: R/reconstruct_network.R
filter_regulation_Rcis | R Documentation |
Refine regulatory relationships through RcisTarget. Before run this function, you should download Gene-motif rankings database from https://resources.aertslab.org/cistarget, and set set the Rankingspath1 as the path of downloaded Gene-motif rankings database.
filter_regulation_Rcis(
Kmeans_result,
regulatory_relationships,
Species,
Rankingsdir,
nesThreshold = 3
)
Kmeans_result |
Kmeans result data.frame, the first column should be 'Symbol' |
regulatory_relationships |
regulatory relationship, generated by |
Species |
character, indicating species of your data, and used to choose annotation file in RcisTarget. Because of the limitaion of RcisTarget, this function only support three species: 'Mm', 'Hs' and 'Fly' |
Rankingsdir |
path of Gene-motif rankings file, which can be downloaded in https://resources.aertslab.org/cistarget. For more details about motif ranking file, you can read https://bioconductor.riken.jp/packages/3.9/bioc/vignettes/RcisTarget/inst/doc/RcisTarget.html#gene-motif_rankings |
nesThreshold |
Numeric. NES threshold to calculate the motif significant (3.0 by default). The NES is calculated -for each motif- based on the AUC distribution of all the motifs for the gene-set (x-mean)/sd. The motifs are considered significantly enriched if they pass the the Normalized Enrichment Score (NES) threshold. |
return filtered regulatory relationship
Rankingspath1 <- 'hg19-500bp-upstream-7species.mc9nr.feather'
# filtered_regulatory_relationships_Rcis <- filter_regulation(Kmeans_result,regulatory_relationships, 'Hs', Rankingspath1)
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