reactome_prep: reactome_prep

In neural-stem-cell-institute/screp: A Package for Enrichment Testing and Visualization of Single Cell RNA-Seq Clusters

reactome_prep

Description

function to make a data to use with visualization function

Usage

reactome_prep(cluster_enriched_df, RP, RP_adj)

Arguments

cluster_enriched_df	data frame produced by enrich_test function
RP	product of RPprep function
RP_adj	Pathway relationship file from Reactome. To decrease time required should limit to organism of interest by selecting for organism, e.g. RPH<-RP[grep("HSA",RPR[,1]),]. Can be modified by user to use some 2nd level terms (e.g. RP_adj<-RPH[-(grep("R-HSA-8953897",RPH[,1])),] ).

Value

returns a data frame for use in the reactome_visualization function

Examples

## Not run: 
RP_ready<-reactome_prep(enrich_results$Enriched_df,RP=RP,RP_adj=mRPR)

## End(Not run)

neural-stem-cell-institute/screp documentation built on Feb. 11, 2023, 10:45 a.m.