consensusSubtyping: Identification of consensus subtypes

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Identification of consensus subtypes

Description

Identification of consensus subtypes

Usage

consensusSubtyping(
  df,
  replicate = 100,
  seed = 1,
  proportion = 0.8,
  adjusted.hypergeometrix.p = F,
  inflation = 2,
  adjacencyMatrixCutoff = NULL,
  subtype.prefix = "CMS",
  pOradjacent = "adjacent",
  inflationConsensus = 0
)

Arguments

df	row is sample, column is study subtype. Plsease note rownames is sample ID
replicate	Default 100
seed	Default 1
proportion	Default 0.8
adjusted.hypergeometrix.p	Default 0.05
inflation	Default 2
adjacencyMatrixCutoff	Default NULL. Cutoff for adjacenty matrix.
pOradjacent	Default "adjacent". Could be p or adjacent. Using p or adjacent to perform mcl cluster
inflationConsensus	Default equal to inflation. inflation is for one boot while inflationConsensus is for subtyping

Examples

data("Subtype.matrix")
res = loonR::consensusSubtyping(Subtype.matrix, replicate = 50)
res$consensus.map

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