Lecture3_One-hundred-software-in-bioinformatics094_ConsensusClusterPlus

Jimmy（jmzeng1314@outlook.com）

Keywords: ConsensusClusterPlus/clust/R/package

#source("http://bioconductor.org/biocLite.R")

#biocLite("ConsensusClusterPlus")

library(ConsensusClusterPlus)

#wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62254/matrix/GSE62254_series_matrix.txt.gz

a=read.table("GSE62254_series_matrix.txt.gz",comment.char = "!",stringsAsFactors=F,header=T)

rownames(a)=a[,1]

a=a[,-1]

#> dim(a)

#[1] 54675 300

d=a

mads=apply(d,1,mad)

d=d[rev(order(mads))[1:5000],]

d = sweep(d,1, apply(d,1,median,na.rm=T))

title="./" #所有的图片以及数据都会输出到这里的

results = ConsensusClusterPlus(as.matrix(d),maxK=6,reps=50,pItem=0.8,pFeature=1,

title=title,clusterAlg="hc",distance="pearson",seed=1262118388.71279,plot="png")

Subtype: 4