filter_regulation_Rcis: Filtering regulatory relationship

In jiang-junyao/IReNA: IReNA

Filtering regulatory relationship

Description

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.

Usage

filter_regulation_Rcis(
  Kmeans_result,
  regulatory_relationships,
  Species,
  Rankingsdir,
  nesThreshold = 3
)

Arguments

Kmeans_result	Kmeans result data.frame, the first column should be 'Symbol'
regulatory_relationships	regulatory relationship, generated by get_cor function
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.

Value

return filtered regulatory relationship

Examples

Rankingspath1 <- 'hg19-500bp-upstream-7species.mc9nr.feather'
 # filtered_regulatory_relationships_Rcis <- filter_regulation(Kmeans_result,regulatory_relationships, 'Hs', Rankingspath1)

jiang-junyao/IReNA documentation built on Nov. 15, 2024, 1:51 a.m.