微環境細胞種羣計數器(MCP-count)方法,該方法允許從轉錄組數據對組織中八種免疫細胞和兩種基質細胞種羣的絕對丰度進行量化。離體免疫組織化學數據支持該方法的有效性。因此此MCP-counter可以用於繪製人類健康組織和非造血人類腫瘤的免疫浸潤的全局圖。MCP-counter也提供R包。從基因表達矩陣中,它爲每個樣本生成 CD3+ T 細胞、CD8+ T 細胞、細胞毒性淋巴細胞、NK 細胞、B 淋巴細胞、源自單核細胞(單核細胞譜系)的細胞、髓樣樹突細胞、中性粒細胞以及內皮細胞和成纖維細胞。MCP-counter 是“單樣本”分數,因爲它們是在每個樣本上獨立計算的。然後,這些分數可用於直接比較隊列中樣本中相應細胞類型的丰度。通過使用石蠟包埋組織切片上免疫組織化學細胞定量對 MCP 計數器進行了定量驗證。結果說明了它在 47 種健康組織類型和 32 種非血液系統惡性腫瘤中評估組織浸潤的成功應用。
該方法可以比較同一個細胞類型在不同sample的丰度,但是不能用於不同細胞類型之間的比較。
#=======================================================
#set the working files and load the packages
#=======================================================
# library(devtools)
# install_github("ebecht/MCPcounter",ref="master", subdir="Source")
##加載包
rm(list=ls())
library(tibble)
library(dplyr)
library(tidyr)
library(MCPcounter)
## 看一下說明書
?MCPcounter.estimate
setwd("/Users/Desktop/p4/geo_sur/geo")
cdata <- read.csv('cdata.csv', header = T, row.names = 1)
cdata[1:20,1:3]
probesets=read.table(curl("http://raw.githubusercontent.com/ebecht/MCPcounter/master/Signatures/probesets.txt"),
sep="\t",stringsAsFactors=FALSE,colClasses="character")
head(probesets)
write.csv(probesets, file = 'probeset.csv')
genes=read.table(curl("http://raw.githubusercontent.com/ebecht/MCPcounter/master/Signatures/genes.txt"),
sep="\t",stringsAsFactors=FALSE,header=TRUE,colClasses="character",check.names=FALSE)
head(genes)
write.csv(genes, file = 'genes.csv')
results<- MCPcounter.estimate(cdata,featuresType=c("HUGO_symbols")[1],
probesets=probesets,
genes=genes)
results <- as.data.frame(results)
results[1:5,1:5]
數據實例:
> cdata[1:5,1:5]
ALCaP01_T ALCaP04_T ALCaP09_T ARM001_T ARM003_T
1-Dec 10.224370 7.393677 7.973883 7.022964 9.849438
1-Mar 11.253553 7.198410 7.810257 8.483075 10.479081
10-Mar 7.798213 6.683564 6.714652 7.057417 9.832400
11-Mar 9.683238 6.729597 7.820598 6.147415 10.207686
2-Mar 21.811216 23.855673 52.646413 24.763275 23.830846
> head(probesets)
V1 V2
1 1557733_a_at T cells
2 1558971_at T cells
3 1558972_s_at T cells
4 1566448_at T cells
5 204777_s_at T cells
6 206485_at T cells
> head(genes)
HUGO symbols Cell population ENTREZID ENSEMBL ID
1 CD28 T cells 940 ENSG00000178562
2 CD3D T cells 915 ENSG00000167286
3 CD3G T cells 917 ENSG00000160654
4 CD5 T cells 921 ENSG00000110448
5 CD6 T cells 923 ENSG00000013725
6 CHRM3-AS2 T cells 100506915 ENSG00000233355
> results[,1:3]
ALCaP01_T ALCaP04_T ALCaP09_T
T cells 14.85268 8.244218 9.812706
CD8 T cells 11.31239 7.389664 8.660349
Cytotoxic lymphocytes 16.07111 7.131069 8.154063
B lineage 20.49535 7.294061 10.610236
NK cells 10.33208 6.910806 7.467822
Monocytic lineage 25.26373 25.752070 14.775617
Myeloid dendritic cells 12.32315 7.533545 9.112773
Neutrophils 14.22642 30.014294 10.082995
Endothelial cells 17.83547 15.691648 15.584108
Fibroblasts 266.52281 125.732827 379.417187