应用两个数据框 [英] Apply over two data frames

问题描述

我使用的是 R，我有两个 data.frames，A 和 B.它们都有 6 行，但 A 有 25000 列(基因)，而 B 有 30 列.我想应用一个带有两个参数的函数 f(x,y) 其中 x 是 A 和 y 的每一列 是 B 的每一列.目前看起来是这样的:

I'm using R, and I have two data.frames, A and B. They both have 6 rows, but A has 25000 columns (genes), and B has 30 columns. I'd like to apply a function with two arguments f(x,y) where x is every column of A and y is every column of B. So far it looks like this:

i = 1
for (x in A){
    j = 1
    for (y in B){
        out[i,j] <- f(x,y)
        j = j + 1
    }
    i = i + 1
}

我对此有两个问题:从我的 Python 编程中，我认为跟踪这样的计数器很笨拙，而从我的 R 编程中，我对 for 循环感到紧张.但是，我不太明白如何将 apply(或者即使我应该应用 apply)应用于这个问题，并希望有人能启发我.我现在需要将 f() 视为原子(实际上是 cor.test()).

I have two issues with this: from my Python programming I associate keeping track of counters like this as crufty, and from my R programming I am nervous of for loops. However, I can't quite see how to apply apply (or even if I should apply apply) to this problem and was hoping someone might enlighten me. I need to treat f() as atomic (it's actually cor.test()) for now.

推荐答案

由于您使用的是数据框，因此使用 lapply 或 sapply 执行此操作可能会更快(特别是考虑到您的数据框的范围).例如，

Since you are using data frames, it might be faster to use lapply or sapply to do this (specially given the scope of your data frames). For example,

x <- data.frame(col1=c(1,2,3,4), col2=c(5,6,7,8), col3=c(9,10,11,12))
y <- data.frame(col1=c(1,2,3,4), col2=c(5,6,7,8))
bl <- lapply(x, function(u){
   lapply(y, function(v){
       f(u,v) # Function with column from x and column from y as inputs
   })
})
out = matrix(unlist(bl), ncol=ncol(y), byrow=T)

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