consensus.MCL: Build a consensus classification using the MCL method

In cit-bioinfo/BuildConsensus: Build a consensus classification from multiple classification methods

Description

Compare and cluster various classification systems applying the same method as in Guinney et al (see reference).

Usage

consensus.MCL(annot.class, I.values = 3.2, outdir, resamp = 0.8,
  n.iter = 1000, pval.cut = 0.001, seed = 42,
  sim.method = c("Jaccard", "CohenKappa")[1], filter.ini = c("fisher",
  "cohenkappa")[1], ck.cut = 0.2)

Arguments

annot.class	Dataframe of samples annotated according to the several classification systems to compare.
I.values	A vector of inflation factors values to use with MCL algorithm. The function running time linearly depends on the given number of values (about 3 minutes for each inflation factor value)
outdir	Path to the directory where to store plots and results. A new directory will be created if the supplied path does not exist.
resamp	Value between 0 and 1. Proportion of samples to use for MCL bootstrap iterations. Default is 0.8.
n.iter	Number of MCL bootstrap iterations for each inflation factor value. Default is 1000.
pval.cut	Cut-off for adjusted P-value to select significant network edges (Fisher test). Default is 0.001
seed	an integer value. See set.seed
sim.method	a string representing the simulation method. One of "Jaccard" or "CohenKappa".
filter.ini	one of "fisher" or "cohenkappa", to be used for initial filtering.
ck.cut	a number between 0 and 1.

Value

A list with the same length of I.values numerical vector. Each element is a list containing the cluster assignments (cl), the co-classification matrix (consensusMat), a subtype stability measure (subtype.stab), the mean weighted average silhouette width (wsil.mean)

Author(s)

Aurelie Kamoun

References

1.Guinney, J. et al. The consensus molecular subtypes of colorectal cancer. Nat Med advance online publication, (2015).

Examples

## Not run: 
#-- Using bladder cancer classes as example
library(BuildConsensus)
data(blca_class)
 
mcl_res <- consensus.MCL(blca_class, outdir = "MCL_res")

## End(Not run)
 

cit-bioinfo/BuildConsensus documentation built on Nov. 27, 2019, 11:29 a.m.