immunedeconv估算免疫细胞比例

immunedeconv：一个R软件包，用于统一访问从大量RNA测序数据估算免疫细胞组分的计算方法。

an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.

1. 安装

conda create -n deconvolution
conda activate deconvolution
conda install -c bioconda -c conda-forge r-immunedeconv

## 连接超时
#install.packages("remotes")
#remotes::install_github("icbi-lab/immunedeconv")

#devtools::install_github('icbi-lab/immunedeconv', repos='http://cran.rstudio.com')

2. 准备表达谱数据

The input data is a gene ×× sample gene expression matrix. In general values should be

• TPM-normalized
• not log-transformed.

gene_expr <- read.table("/data/query_expr_ready.txt",
                        sep='\t',header=T)

head(gene_expr)

colnames(gene_expr)
rownames(gene_expr)

rownames(gene_expr) <- gene_expr$ID

gene_expr <- gene_expr[,-1]
exprs_matrix <- as.matrix(gene_expr)
head(exprs_matrix)

3. 估算免疫细胞比例

library(tidyr)
library(immunedeconv)

res = deconvolute(exprs_matrix, "quantiseq")

res = deconvolute(exprs_matrix, "quantiseq") %>%
  map_result_to_celltypes(c("T cell CD4+"), "quantiseq")

knitr::kable(res, digits=2)

res1 <- deconvolute(your_mixture_matrix, "mcp_counter")

res2 <- deconvolute(your_mixture_matrix, "xcell")

res3 <- deconvolute(your_mixture_matrix, "epic")

## method: 
#quantiseq
#timer
#cibersort
#cibersort_abs
#mcp_counter
#xcell
#epic

参考：

https://github.com/icbi-lab/immunedeconv