Groups_Sup: cluster the samples

In AutoPipe: Automated Transcriptome Classifier Pipeline: Comprehensive Transcriptome Analysis

Description

This function clusters the samples into x clusters.

Usage

Groups_Sup(me_TOP, me, number_of_k,TRw)

Arguments

me_TOP	the matrix with the n top genes, usually the from output of the function TopPAM
me	the original expression matrix. (with genes in rows and samples in columns).
number_of_k	the number of clusters
TRw	threshold for the elemenation of the samples with a Silhouette width lower than TRw. Default value is -1.

Examples

## load data
library(org.Hs.eg.db)
data(rna)
me_x=rna
res<-AutoPipe::TopPAM(me_x,max_clusters = 8, TOP=100)
me_TOP=res[[1]]
number_of_k=res[[3]]
File_genes=Groups_Sup(me_TOP, me=me_x, number_of_k,TRw=-1)
groups_men=File_genes[[2]]
me_x=File_genes[[1]]

AutoPipe documentation built on May 1, 2019, 7:28 p.m.