Question

我正在创建并附加到R中的数据框：

dat <- data.frame(nodeA = character(), nodeB = character(), edge = numeric())
for (i in 1:length(countTable)-1){
  for (j in i+1:length(countTable)){
    vecA = as.numeric(as.character(countTable[i,]))
    vecB = as.numeric(as.character(countTable[j,]))
    nodeA = row.names(countTable[i,])
    nodeB = row.names(countTable[j,])
    corCoeff = cor(vecA , vecB , method = "spearman")
    dat = rbind(dat, data.frame(nodeA = nodeA, nodeB = nodeB, edge = corCoeff))
  }
}

countTable的头部和结构如下：

> head(countTable)
                Norm One Two Three Four
ENST00000000233   12  28  11     4    8
ENST00000000412   23  44  37    23   45
ENST00000000442    9  12  27    10   22
ENST00000001008   18  98  61    21   31
ENST00000001567   16   7   3     9   12
ENST00000002125    2   4   4     5    1

> str(countTable)
'data.frame':   17972 obs. of  5 variables:
 $ Norm : int  12 23 9 18 16 2 4 1 22 14 ...
 $ One  : int  28 44 12 98 7 4 24 14 39 39 ...
 $ Two  : int  11 37 27 61 3 4 12 3 69 30 ...
 $ Three: int  4 23 10 21 9 5 4 3 271 9 ...
 $ Four : int  8 45 22 31 12 1 13 7 123 60 ...

如果我单独查看嵌套for循环中的代码，它就像我希望的那样工作。但是，当我运行整个代码时，我收到一个错误：

Error in data.frame(nodeA = nodeA, nodeB = nodeB, edge = corCoeff) : 
  arguments imply differing number of rows: 0, 1
In addition: Warning message:
NAs introduced by coercion

Answer 1

:运算符的优先级高于+和-。您的代码应更正为：

for (i in 1:(length(countTable)-1)){
   for (j in (i+1):length(countTable)){
      ...
   }
}

注意：

之间的区别

n <- 3
for (i in 1:n-1)
  for (j in i+1:n)
    cat(sprintf("(%g,%g)\n", i, j))
## (0,1)
## (0,2)
## (0,3)
## (1,2)
## (1,3)
## (1,4)
## (2,3)
## (2,4)
## (2,5)

和

for (i in 1:(n-1))
  for (j in (i+1):n)
    cat(sprintf("(%g,%g)\n", i, j))
## (1,2)
## (1,3)
## (2,3)

Answer 2

你可能想要这样的东西。将countTable转换为matrix并下拉到一个循环，使用i和i-1作为循环索引。并且无需事先创建空数据框。

> countTable <- as.matrix(countTable)
> rn <- rownames(countTable)
> dat <- do.call(rbind, lapply(2:nrow(countTable), function(i){
    corCoeff <- cor(countTable[i-1,] , countTable[i,], 
                    method = "spearman", use = "complete.obs")
    data.frame(nodeA = rn[i-1], nodeB = rn[i], edge = corCoeff)
    }))
> dat
#             nodeA           nodeB       edge
# 1 ENST00000000233 ENST00000000412  0.1538968
# 2 ENST00000000412 ENST00000000442  0.6668859
# 3 ENST00000000442 ENST00000001008  0.7000000
# 4 ENST00000001008 ENST00000001567 -0.8000000
# 5 ENST00000001567 ENST00000002125 -0.5642881

在R中创建和附加到数据框（错误：参数意味着不同的行数：0,1）

2 个答案: