人和小鼠的基因怎么无缝切换？

用户11414625

发布于 2024-12-27 16:56:16

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文章被收录于专栏：生信星球520生信星球520

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问题

今天给生信入门班和数据挖掘班的往期学员提供直播答疑遇到了一个好问题，给大家分享下。

学员使用的是小鼠的数据

想要使用曾老师提供的marker基因，但那些基因是人的。

人和小鼠基因名字粗略对应，就是人基因名都是大写，而小鼠是首字母大写！

因此我们就需要把每个基因名字变成首字母大写咯！

批量转换

cell_type_markers<-list(
     Cardiomyocytes=c("ACTC1","MYL7","TNNT2"),
     Fibroblasts=c("DCN","GSN","COL1A2"),
     EndothelialCells=c("VWF","CD36"),
     Pericytes=c("RGS5","ABCC9"),
     SmoothMuscleCells=c("ACTA2","MYH11","MYLK"),
     Macrophages=c("CD163","C1QA"),
     Lymphocytes=c("NKG7","CCL5","IL7R"),
     Monocytes=c("S100A8"),
     BCells=c("CD69","CD79A"),
     MesothelialCells=c("MSLN")
)

cell_type_markers

## $Cardiomyocytes
## [1] "ACTC1" "MYL7"  "TNNT2"
## 
## $Fibroblasts
## [1] "DCN"    "GSN"    "COL1A2"
## 
## $EndothelialCells
## [1] "VWF"  "CD36"
## 
## $Pericytes
## [1] "RGS5"  "ABCC9"
## 
## $SmoothMuscleCells
## [1] "ACTA2" "MYH11" "MYLK" 
## 
## $Macrophages
## [1] "CD163" "C1QA" 
## 
## $Lymphocytes
## [1] "NKG7" "CCL5" "IL7R"
## 
## $Monocytes
## [1] "S100A8"
## 
## $BCells
## [1] "CD69"  "CD79A"
## 
## $MesothelialCells
## [1] "MSLN"

所以如果强行使用，当然是一个基因都找不到咯！后面就会进行不下去

那咋整呢。我们可以用R语言技巧把基因名改为首字母大写。

一句搞定:

library(stringr)
cell_type_markers = lapply(cell_type_markers, str_to_title) 
cell_type_markers

## $Cardiomyocytes
## [1] "Actc1" "Myl7"  "Tnnt2"
## 
## $Fibroblasts
## [1] "Dcn"    "Gsn"    "Col1a2"
## 
## $EndothelialCells
## [1] "Vwf"  "Cd36"
## 
## $Pericytes
## [1] "Rgs5"  "Abcc9"
## 
## $SmoothMuscleCells
## [1] "Acta2" "Myh11" "Mylk" 
## 
## $Macrophages
## [1] "Cd163" "C1qa" 
## 
## $Lymphocytes
## [1] "Nkg7" "Ccl5" "Il7r"
## 
## $Monocytes
## [1] "S100a8"
## 
## $BCells
## [1] "Cd69"  "Cd79a"
## 
## $MesothelialCells
## [1] "Msln"