subtypeAssociationAnalysis: Subtype association: Calculate Jaccard similarity coefficient...

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Subtype association: Calculate Jaccard similarity coefficient and perform hypergeometrix test

Description

Subtype association: Calculate Jaccard similarity coefficient and perform hypergeometrix test

Usage

subtypeAssociationAnalysis(
  df,
  concateStudy = F,
  adjusted.hypergeometrix.p = F,
  cut.edge.byPval = 0.05,
  print.message = T
)

Arguments

df	row is sample, column is study subtype. Plsease note rownames is sample ID
concateStudy	If to add study name (from colnames) into result
adjusted.hypergeometrix.p	Default FALSE, if to adjust hypergeometrix P value by BH method.
cut.edge.byPval	Default 0.05
print.message	If print message

Examples

data(Subtype.matrix)
res <- loonR::subtypeAssociationAnalysis(Subtype.matrix)
res$hyperGeoTest.Analysis

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.