匹配和计算 R 中的数据矩阵 [英] Match and Count the Data Matrix in R

问题描述

数据集如下所示:

 Gene SampleName
gene1    sample1
gene1    sample2
gene1    sample3
gene2    sample2
gene2    sample3
gene2    sample4
gene3    sample1
gene3    sample5

我的目标是制作这样的数据矩阵:

My goal is to make a data matrix like this:

       gene1 gene2 gene3
gene1      -     2     1
gene2      -     -     0
gene3      -     -     -

gene1 vs gene2 是 2 因为它们共享相同的样本 sample2 和 sample3.gene1 vs gene3 是 1，因为它们只共享一个相同的样本 - sample1.

gene1 vs gene2 is 2 because they share the same samples sample2 and sample3. gene1 vs gene3 is 1 because they only share one same sample - sample1.

我的问题是如何在 R 或 Perl 中实现这个目标?实际数据集要大得多.我非常感谢您的帮助.

My question is how can I achieve this goal in R or Perl? The actual data set is much larger. I highly appreciate your help.

这是 R 的 dput(df) 输出:

Here's the dput(df) output for R:

df <- structure(list(Gene = c("gene1", "gene1", "gene1", "gene2", "gene2", 
"gene2", "gene3", "gene3"), SampleName = c("sample1", "sample2", 
"sample3", "sample2", "sample3", "sample4", "sample1", "sample5"
)), .Names = c("Gene", "SampleName"), row.names = c(NA, -8L), class = "data.frame")

推荐答案

你可以查看crossprod(或tcrossprod)函数和table代码>:

You can look at the crossprod (or tcrossprod) function along with table:

out <- tcrossprod(table(df))
out
#        Gene
# Gene    gene1 gene2 gene3
#   gene1     3     2     1
#   gene2     2     3     0
#   gene3     1     0     2

放下对角线和下三角形以获得您显示的确切输出.

Drop the diagonal and the lower-triangle to get the exact output you show.

diag(out) <- NA
out[lower.tri(out)] <- NA
print.table(out)  ## print.table deals with NAs differently
#        Gene
# Gene    gene1 gene2 gene3
#   gene1           2     1
#   gene2                 0
#   gene3                  

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