Introduction

The following are the codes for classifying the samples according to the distance from the centroids of reference class.

Code exmaple

library(data.table)
centroids <- read.table("data/other/GSE10886/pam50_centroids.txt")
gene_name <- fread("data/other/GSE10886/pam_gene_name.txt", header = T)
rownames(centroids) <- gene_name[data.table(pcrID = rownames(centroids)), GeneName, on = "pcrID"]  # Get gene name

# Get intersect genes between my data and centoid data
inter_gene <- intersect(rownames(centroids), rownames(mt))
dat <- mt[inter_gene,]
centroids <- centroids[inter_gene,]

# Calculaed dist
d1=apply(centroids,2,function(i){
  dist(t(cbind(i,dat)))[1:ncol(dat)]
})
# Select the classe with min distance
p1=apply(d1,1, function(x){
  colnames(d1)[which.min(x)]
})

 p1  # Predicted class

References

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Original

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