UseMethod(generic = “FindMarkers“, object = object)获取FindMarkers的源代码

今天在使用Seurat包的时候，想看看Findmarker的源代码写了什么，于是用了

getAnywhere(FindMarkers)

来查看源代码，但是却反回了：

A single object matching ‘FindMarkers’ was found
It was found in the following places
  package:Seurat
  namespace:Seurat
with value

function (object, ...) 
{
    UseMethod(generic = "FindMarkers", object = object)
}
<bytecode: 0x1185eaf0>
<environment: namespace:Seurat>

没有具体显示Findmarker的内容。

以下是解决办法：

FindMarkers是一个泛型函数，需要找到适用于特定对象类型的方法。

使用getMethod函数获取特定方法的实现，然后查看其源代码。

# 列出FindMarkers泛型函数的所有方法
methods("FindMarkers")
# [1] FindMarkers.Assay*    FindMarkers.default*  FindMarkers.DimReduc* 
# FindMarkers.SCTAssay* FindMarkers.Seurat*  
# see '?methods' for accessing help and source code

这将显示所有可用的FindMarkers函数的方法。

一旦确定了特定方法，就可以使用getMethod来查看其源代码。例如，如果使用的是Seurat对象：

# 获取Seurat类的特定方法
method <- getMethod("FindMarkers", "Seurat")

# 打印方法的源代码
print(method)

或者：

getAnywhere(FindMarkers.Seurat)

最终得到结果：

A single object matching ‘FindMarkers.Seurat’ was found
It was found in the following places
  registered S3 method for FindMarkers from namespace Seurat
  namespace:Seurat
with value

function (object, ident.1 = NULL, ident.2 = NULL, group.by = NULL, 
    subset.ident = NULL, assay = NULL, slot = "data", reduction = NULL, 
    features = NULL, logfc.threshold = 0.25, test.use = "wilcox", 
    min.pct = 0.1, min.diff.pct = -Inf, verbose = TRUE, only.pos = FALSE, 
    max.cells.per.ident = Inf, random.seed = 1, latent.vars = NULL, 
    min.cells.feature = 3, min.cells.group = 3, mean.fxn = NULL, 
    fc.name = NULL, base = 2, densify = FALSE, ...) 
{
    if (!is.null(x = group.by)) {
        if (!is.null(x = subset.ident)) {
            object <- subset(x = object, idents = subset.ident)
        }
        Idents(object = object) <- group.by
    }
    if (!is.null(x = assay) && !is.null(x = reduction)) {
        stop("Please only specify either assay or reduction.")
    }
    if (length(x = ident.1) == 0) {
        stop("At least 1 ident must be specified in `ident.1`")
    }
    if (is.null(x = reduction)) {
        assay <- assay %||% DefaultAssay(object = object)
        data.use <- object[[assay]]
        cellnames.use <- colnames(x = data.use)
    }
    else {
        data.use <- object[[reduction]]
        cellnames.use <- rownames(x = data.use)
    }
    cells <- IdentsToCells(object = object, ident.1 = ident.1, 
        ident.2 = ident.2, cellnames.use = cellnames.use)
    if (!is.null(x = latent.vars)) {
        latent.vars <- FetchData(object = object, vars = latent.vars, 
            cells = c(cells$cells.1, cells$cells.2))
    }
    norm.command <- paste0("NormalizeData.", assay)
    norm.method <- if (norm.command %in% Command(object = object) && 
        is.null(x = reduction)) {
        Command(object = object, command = norm.command, value = "normalization.method")
    }
    else if (length(x = intersect(x = c("FindIntegrationAnchors", 
        "FindTransferAnchors"), y = Command(object = object)))) {
        command <- intersect(x = c("FindIntegrationAnchors", 
            "FindTransferAnchors"), y = Command(object = object))[1]
        Command(object = object, command = command, value = "normalization.method")
    }
    else {
        NULL
    }
    de.results <- FindMarkers(object = data.use, slot = slot, 
        cells.1 = cells$cells.1, cells.2 = cells$cells.2, features = features, 
        logfc.threshold = logfc.threshold, test.use = test.use, 
        min.pct = min.pct, min.diff.pct = min.diff.pct, verbose = verbose, 
        only.pos = only.pos, max.cells.per.ident = max.cells.per.ident, 
        random.seed = random.seed, latent.vars = latent.vars, 
        min.cells.feature = min.cells.feature, min.cells.group = min.cells.group, 
        mean.fxn = mean.fxn, base = base, fc.name = fc.name, 
        densify = densify, norm.method = norm.method, ...)
    return(de.results)
}
<bytecode: 0xc38b748>
<environment: namespace:Seurat>