TopPAM {AutoPipe}

Compute Top genes

Description

This function computes the n=TOP genes and the the best number of clusters

Usage

TopPAM(me, max_clusters=15,TOP=1000,B=100,clusterboot=FALSE)

Arguments

me

a matrix with genes in rows and samples in columns

max_clusters

max. number of clusters to check

TOP

the number of genes to take.

B

integer, number of Monte Carlo (“bootstrap”) samples.

clusterboot

A logical value indicating wether or not to calculate the Gap statistic and to bootstrap.

Details

we use the clusGap algorithm from the package cluster to calculate the Gap statistic.

Value

a list of 1. A matrix with the top genes 2. A list of means of the Silhouette width for each number of clusters. 3. The optimal number of clusters. 4. gap_st the gap statistic of the clustering 5. best number of clusters according to the gap statistic.

Examples

##load the org.Hs.eg Library
library(org.Hs.eg.db)
#' ## load data
data(rna)
me_x=rna
res<-AutoPipe::TopPAM(me_x,max_clusters = 8, TOP=100,clusterboot=FALSE)
me_TOP=res[[1]]
number_of_k=res[[3]]