问题

Here is the translated code portion:

我有一个包含RNA、细胞表面蛋白(ADT)测定和元数据的单细胞多组学Seurat对象。
我基于感兴趣的ADT水平对对象进行了子集化。我想添加元数据以在原始对象内特定地注释这些子集。

我尝试的方法不起作用：

```R
data[subset]

出现错误：

Error in as.character.default(x) : 
  no method for coercing this S4 class to a vector

或者 data@assays$ADT[subset]

出现错误：

Error in GetAssayData(object = x)[i, j, ..., drop = FALSE] : 
  invalid or not-yet-implemented 'Matrix' subsetting

或者 data@meta.data[subset] 或 data@meta.data[[subset]]

出现错误：

Error in `[.default`(data@meta.data, subset) : 
  invalid subscript type 'S4'

任何帮助将不胜感激，谢谢。

更新：使用以下方法可以解决：

# 为每个子集添加注释
subset1@meta.data$newLabel <- "subset1"
subset2@meta.data$newLabel <- "subset2"
subset3@meta.data$newLabel <- "subset3"
subset4@meta.data$newLabel <- "subset4"  

# 合并子集的元数据的函数
multiannot <- function(x)
{
  CellsName <- NULL
  for(i in 1: length(x))
  {
    CellsNameInt <- subset(x[[i]]@meta.data, select = c("newLabel"))
    if(is.null(CellsName) == FALSE)
      CellsName <- rbind(CellsName, CellsNameInt)
    else
      CellsName <- CellsNameInt
  }
  return(CellsName)
}

# 使用包含子集的向量调用该函数
metadatanew <- multiannot(c(subset1, subset2, subset3, subset4))

# 将元数据添加到原始对象
data <- AddMetaData(data, metadatanew)

<details>
<summary>英文:</summary>

I have a single-cell multi-omic Seurat object that contains RNA, cell-surface-protein(ADT) assays and metadata.
I subsetted the object based on ADT levels of interest. I want to add metadata to annotate these subsets specifically within the original object.

What I tried does not work:

data[subset]

gives the error:

Error in as.character.default(x) :
no method for coercing this S4 class to a vector

Or data@assays$ADT[subset]

Error in GetAssayData(object = x)[i, j, ..., drop = FALSE] :
invalid or not-yet-implemented 'Matrix' subsetting

Or data@meta.data[subset] OR data@meta.data[[subset]]

Error in [.default(data@meta.data, subset) :
invalid subscript type 'S4'

Any help would be appreciated, thank you.

UPDATE: It works using the approach:

add annotation to each subset

subset1@meta.data$newLabel<-"subset1"
subset2@meta.data$newLabel<-"subset2"
subset3@meta.data$newLabel<-"subset3"
subset4@meta.data$newLabel<-"subset4"

function that merges the metadata of the subsets

multiannot<-function(x)
{
  CellsName<-NULL
  for(i in 1: length(x))
  {
    CellsNameInt <- subset(x[[i]]@meta.data, select = c("newLabel"))
    if(is.null(CellsName)==F)
      CellsName <-rbind(CellsName,CellsNameInt) else
        CellsName <- CellsNameInt
  }
  return(CellsName)
}

call the function using a vector that contains the subsets

metadatanew<-multiannot(c(subset1,subset2,subset3,subset4))

add the metadata to the original object

data<-AddMetaData(data, metadatanew)

</details>


# 答案1
**得分**: 1

根据我理解你的问题已经在这里得到了答案：
https://stackoverflow.com/questions/42279766/add-metadata-to-seurat-object?rq=1

我假设你已经成功地根据你在问题中写的内容对你的对象进行了子集化。
将元数据添加回原始对象的一种方法如下：

```R
CellsMetaTrim <- subset(data@meta.data, select = c("name_of_column"))
# data是你的仅包含ADT的Seurat对象

# "name_of_column"是你想要从ADT数据集传递到包含所有细胞的对象的注释列的名称

head(CellsMetaTrim)

All_Data_Atlas <- AddMetaData(All_Data_Atlas, CellsMetaTrim)
# All_Data_Atlas是包含所有细胞的Seurat对象

让我知道它是否有效

或者，如果你的对象中有一个区分ADT和非ADT的所有细胞的元数据列，你还可以创建一个新的元数据列并在该列中修改它，如果它与该列中的某个值匹配：

All_Data_Atlas$newLabel <- as.character(All_Data_Atlas$orig.ident)
# orig.ident是你已经标记了ADT的元数据列
# $newLabel是新元数据的列
All_Data_Atlas$newLabel <- replace(All_Data_Atlas$newLabel, All_Data_Atlas$newLabel %in% "ADT", "New_Information")

如果你想要从多个数据集中添加元数据，你可以在CellsMetaTrim上使用rbind：
首先确保所有数据集都具有要添加的数据列的匹配列名，如果需要，你可以通过创建新列来完成这一点：

data$newLabel <- data1$oldLabel1
data$newLabel <- data2$oldLabel2

# 然后获得多个CellsMetaTrim并将它们绑在一起：
CellsMetaTrim1 <- subset(data@meta.data, select = c("newLabel"))
CellsMetaTrim2 <- subset(data@meta.data, select = c("newLabel"))
CellsMetaTrim <- rbind(CellsMetaTrim2, CellsMetaTrim1)

# 现在你可以将它添加到你的数据集中
All_Data_Atlas <- AddMetaData(All_Data_Atlas, CellsMetaTrim)

    CellsMetaTrim <- subset(data@meta.data, select = c("name_of_column"))
    #data is your seurat object with only ADT

    #"name_of_column" is the name of the annotation column you want to transfer from ADT data set to the object will all your cells.

    head(CellsMetaTrim)

    All_Data_Atlas <- AddMetaData(All_Data_Atlas, CellsMetaTrim)
    #All_Data_Atlas is the seurat object with all the cells.

     All_Data_Atlas$newLabel <- as.character(All_Data_Atlas$orig.ident)
     #orig.ident is the metadata column where you have labelled ADT from the other cells
     #$newLabel is the column for the new metadata
     All_Data_Atlas$newLabel  <- replace(All_Data_Atlas$newLabel, All_Data_Atlas$newLabel %in% "ADT", "New_Information")

data$newLabel <- data1$oldLabel1 
data$newLabel <- data2$oldLabel2 
#Then obtain multiple CellsMetaTrim and bind them together:
CellsMetaTrim1 <- subset(data@meta.data, select = c("newLabel")) 
CellsMetaTrim2 <- subset(data@meta.data, select = c("newLabel")) 
CellsMetaTrim<-rbind(CellsMetaTrim2,CellsMetaTrim1) 
#Now you can add it to your dataset
All_Data_Atlas <- AddMetaData(All_Data_Atlas, CellsMetaTrim)