匹配并计算R中的数据矩阵

Question

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

我的目标是创建一个这样的数据矩阵:

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

gene1vs gene2是2因为他们共享相同的样本sample2和sample3.gene1vs gene3是1,因为他们只共享一个相同的样本 - sample1.

我的问题是如何在R或Perl中实现这一目标？实际数据集要大得多.我非常感谢你的帮助.

---

这是dput(df)R 的输出:

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")

Answer 1

您可以查看crossprod(或tcrossprod)函数以及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.

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