2018年的Nature 上公開了一份尿路上皮癌（BLCA）的免疫治療隊列數(shù)據(jù)，而這份數(shù)據(jù)就儲存在IMvigor210CoreBiologies包中。下面就來學習下吧

1.IMvigor210CoreBiologies包安裝

從(http://research-pub.gene.com/IMvigor210CoreBiologies/packageVersions/)下載后本地安裝。注意：安裝過程中需要很多依賴包，逐步安裝即可。

rm(list = ls())
library(pacman)
# p_load(DESeq, lsmeans, spatstat)
# install.packages("D:/Database/IMvigor210/IMvigor210CoreBiologies_1.0.0.tar.gz",repos = NULL)
# install.packages("D:/Database/IMvigor210/DESeq_1.38.0.tar.gz",repos = NULL)
library(IMvigor210CoreBiologies)

2.數(shù)據(jù)預處理

2.1 表達矩陣

library(IMvigor210CoreBiologies)
data(cds)
expMatrix <- counts(cds)
eff_length2 <- fData(cds)[,c("entrez_id","length","symbol")]
rownames(eff_length2) <- eff_length2$entrez_id
head(eff_length2)
feature_ids <- rownames(expMatrix)
expMatrix <- expMatrix[feature_ids %in% rownames(eff_length2),]
mm <- match(rownames(expMatrix),rownames(eff_length2))
eff_length2 <- eff_length2[mm,]

x <- expMatrix/eff_length2$length
eset <- t(t(x)/colSums(x))*1e6
summary(duplicated(rownames(eset)))

eset <- IOBR::anno_eset(eset = eset,
                        annotation = eff_length2,
                        symbol = "symbol",
                        probe = "entrez_id",
                        method = "mean")
tumor_type <- "blca"
if(max(eset)>100) eset <- log2(eset+1)

2.2 表型文件

pdata <- pData(cds)
colnames(pdata) <- gsub(colnames(pdata),pattern = " ",replacement = "_")
pdata <- rownames_to_column(pdata[,c("binaryResponse",
                                     "FMOne_mutation_burden_per_MB",
                                     "Neoantigen_burden_per_MB",
                                     "censOS","os")],var = "ID")
colnames(pdata)<-c("ID","BOR_binary","TMB","TNB","status","time")
pdata<-pdata[!is.na(pdata$BOR_binary),]
pdata$BOR_binary<-ifelse(pdata$BOR_binary=="CR/PR","R","NR")
save(expMatrix,pdata,file = "expcli_IMvigor210.Rdata")

最后得到表達矩陣和表型文件：

3.文章實戰(zhàn)

有了表達矩陣，預后數(shù)據(jù)，可以像下面這篇文章來展示分型、riskScore等結果對免疫反應的影響。

備注：IMvigor210CoreBiologies數(shù)據(jù)的處理過程參考自IOBR包的說明文檔，大家使用時注意引用。
參考文獻：
1.IOBR: Immuno-Oncology Biological Research
2.Characterization of the Immune Cell Infiltration Landscape in Head and Neck
Squamous Cell Carcinoma to Aid Immunotherapy