Map the gene set of interest to the known pathways

Map the gene set of interest to the known pathways

Map2Pathways(
  partcorr.list,
  conditions = NULL,
  GeneInterest = NULL,
  pathwayRef,
  pathwayRef_geneVariable,
  pathwayRef_pathVariable,
  threshold = 0
)

Arguments

partcorr.list	a list of estimated partial correlation matrices
conditions	a vector of the names of the corresponding partial correlation matrices
GeneInterest	character. e.g. "MYC"
pathwayRef	a data frame, including the gene and pathway information. e.g. column1 is genes, column2 is the pathways this gene belongs to according to Sigma.Mini.Map
pathwayRef_geneVariable	character, the column name of gene variable
pathwayRef_pathVariable	character, the column name of pathway variable
threshold	the cutoff value for partial correlation, for visualization and GSEA purpose.

Value

x.connect: the list of genes that connected to the GeneInterest under each condition

GSEA.table: the final GSEA table