计算foldchange时Error in names(x) ＜- value:‘names‘ attribute[3]must be the same length as the vector[2]

Seurat计算foldchange时报错Error in names(x) <- value : 'names' attribute [3] must be the same length as the vector [2]

起初，在计算一个数据的peak fc 时发现这个报错Error in names(x) <- value : 'names' attribute [3] must be the same length as the vector [2]，在网上查了很多方法都没有解决，于是打算跑一遍signac官方教程，在官方教程中计算到peak fc 时也是一样报错，于是想到可能不是个人数据原因，而是环境或者包的问题，后面查看排除后发现是seurat包这个FoldChange()这个函数有bug，在目前新版seurat v5.01中得到解决：

查看当前包版本：

packageVersion("Seurat") #4.3.0.1 old for now

packageVersion("Signac") #1.6.0

旧版代码： 

#Unuseful function from seurat v4.3.0.1 <seurat/R/differential_expression.R, line 1182>
FoldChange.Seurat <- function(
  object,
  ident.1 = NULL,
  ident.2 = NULL,
  group.by = NULL,
  subset.ident = NULL,
  assay = NULL,
  slot = 'data',
  reduction = NULL,
  features = NULL,
  pseudocount.use = NULL,
  mean.fxn = NULL,
  base = 2,
  fc.name = NULL,
  ...
) {
  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.")
  }
  # select which data to use
  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(data.use)
  }
  cells <- IdentsToCells(
    object = object,
    ident.1 = ident.1,
    ident.2 = ident.2,
    cellnames.use = cellnames.use
  )
  fc.results <- FoldChange(
    object = data.use,
    cells.1 = cells$cells.1,
    cells.2 = cells$cells.2,
    features = features,
    slot = slot,
    pseudocount.use = pseudocount.use,
    mean.fxn = mean.fxn,
    base = base,
    fc.name = fc.name
  )
  return(fc.results)
}

IdentsToCells <- function(
  object,
  ident.1,
  ident.2,
  cellnames.use
) {
  #
  if (is.null(x = ident.1)) {
    stop("Please provide ident.1")
  } else if ((length(x = ident.1) == 1 && ident.1[1] == 'clustertree') || is(object = ident.1, class2 = 'phylo')) {
    if (is.null(x = ident.2)) {
      stop("Please pass a node to 'ident.2' to run FindMarkers on a tree")
    }
    tree <- if (is(object = ident.1, class2 = 'phylo')) {
      ident.1
    } else {
      Tool(object = object, slot = 'BuildClusterTree')
    }
    if (is.null(x = tree)) {
      stop("Please run 'BuildClusterTree' or pass an object of class 'phylo' as 'ident.1'")
    }
    ident.1 <- tree$tip.label[GetLeftDescendants(tree = tree, node = ident.2)]
    ident.2 <- tree$tip.label[GetRightDescendants(tree = tree, node = ident.2)]
  }
  if (length(x = as.vector(x = ident.1)) > 1 &&
      any(as.character(x = ident.1) %in% cellnames.use)) {
    bad.cells <- cellnames.use[which(x = !as.character(x = ident.1) %in% cellnames.use)]
    if (length(x = bad.cells) > 0) {
      stop(paste0("The following cell names provided to ident.1 are not present in the object: ", paste(bad.cells, collapse = ", ")))
    }
  } else {
    ident.1 <- WhichCells(object = object, idents = ident.1)
  }
  # if NULL for ident.2, use all other cells
  if (length(x = as.vector(x = ident.2)) > 1 &&
      any(as.character(x = ident.2) %in% cellnames.use)) {
    bad.cells <- cellnames.use[which(!as.character(x = ident.2) %in% cellnames.use)]
    if (length(x = bad.cells) > 0) {
      stop(paste0("The following cell names provided to ident.2 are not present in the object: ", paste(bad.cells, collapse = ", ")))
    }
  } else {
    if (is.null(x = ident.2)) {
      ident.2 <- setdiff(x = cellnames.use, y = ident.1)
    } else {
      ident.2 <- WhichCells(object = object, idents = ident.2)
    }
  }
  return(list(cells.1 = ident.1, cells.2 = ident.2))
}

新版代码：

#Useful function from seurat v5.0.1 <seurat/R/differential_expression.R, line1314>
FoldChange.Seurat <- function(
  object,
  ident.1 = NULL,
  ident.2 = NULL,
  group.by = NULL,
  subset.ident = NULL,
  assay = NULL,
  slot = 'data',
  reduction = NULL,
  features = NULL,
  pseudocount.use = 1,
  mean.fxn = NULL,
  base = 2,
  fc.name = NULL,
  ...
) {
  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.")
  }
  # select which data to use
  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(data.use)
  }
  cells <- IdentsToCells(
    object = object,
    ident.1 = ident.1,
    ident.2 = ident.2,
    cellnames.use = cellnames.use
  )
  # check normalization method
  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
  }
  fc.results <- FoldChange(
    object = data.use,
    cells.1 = cells$cells.1,
    cells.2 = cells$cells.2,
    features = features,
    slot = slot,
    pseudocount.use = pseudocount.use,
    mean.fxn = mean.fxn,
    base = base,
    fc.name = fc.name,
    norm.method = norm.method
  )
  return(fc.results)
}

IdentsToCells <- function(
  object,
  ident.1,
  ident.2,
  cellnames.use
) {
  #
  if (is.null(x = ident.1)) {
    stop("Please provide ident.1")
  } else if ((length(x = ident.1) == 1 && ident.1[1] == 'clustertree') || is(object = ident.1, class2 = 'phylo')) {
    if (is.null(x = ident.2)) {
      stop("Please pass a node to 'ident.2' to run FindMarkers on a tree")
    }
    tree <- if (is(object = ident.1, class2 = 'phylo')) {
      ident.1
    } else {
      Tool(object = object, slot = 'BuildClusterTree')
    }
    if (is.null(x = tree)) {
      stop("Please run 'BuildClusterTree' or pass an object of class 'phylo' as 'ident.1'")
    }
    ident.1 <- tree$tip.label[GetLeftDescendants(tree = tree, node = ident.2)]
    ident.2 <- tree$tip.label[GetRightDescendants(tree = tree, node = ident.2)]
  }
  if (length(x = as.vector(x = ident.1)) > 1 &&
      any(as.character(x = ident.1) %in% cellnames.use)) {
    bad.cells <- cellnames.use[which(x = !as.character(x = ident.1) %in% cellnames.use)]
    if (length(x = bad.cells) > 0) {
      stop(paste0("The following cell names provided to ident.1 are not present in the object: ", paste(bad.cells, collapse = ", ")))
    }
  } else {
    ident.1 <- WhichCells(object = object, idents = ident.1)
  }
  # if NULL for ident.2, use all other cells
  if (length(x = as.vector(x = ident.2)) > 1 &&
      any(as.character(x = ident.2) %in% cellnames.use)) {
    bad.cells <- cellnames.use[which(!as.character(x = ident.2) %in% cellnames.use)]
    if (length(x = bad.cells) > 0) {
      stop(paste0("The following cell names provided to ident.2 are not present in the object: ", paste(bad.cells, collapse = ", ")))
    }
  } else {
    if (is.null(x = ident.2)) {
      ident.2 <- setdiff(x = cellnames.use, y = ident.1)
    } else {
      ident.2 <- WhichCells(object = object, idents = ident.2)
    }
  }
  return(list(cells.1 = ident.1, cells.2 = ident.2))
}

可以看出增加了check normalization method这一模块，具体原因还不知道