R中行名矩阵的慢子集

对于一个大矩阵,我只想保留包含在额外向量中的某些行。此向量包含矩阵的一些行名。

我用了一个 microbenchmark 比较四种不同的解决方案,但我想知道在R中是否存在更快的解决方案。

m <- matrix(rnorm(1e8), nrow = 1e4, ncol = 1e4)
rownames(m) <- paste0("row_", seq(1:nrow(m)))
dim(m); m[1:5, 1:5]
include_list <- paste0("row_", ceiling(runif(1000, 1, 1e4))) # rows to keep

library(microbenchmark)
microbenchmark(
  m1 <- m[rownames(m) %in% include_list, , drop = FALSE],
  m2 <- m[include_list, , drop = FALSE],
  m3 <- m[match(include_list, rownames(m)), , drop = FALSE],
  m4 <- subset(m, rownames(m) %in% include_list)
)

以下是测试结果 :

Unit: milliseconds
                                                      expr      min       lq     mean   median       uq      max neval cld
 m3 <- m[match(include_list, rownames(m)), , drop = FALSE] 251.9575 258.0483 279.9949 266.1691 284.8803 422.3918   100   b
                     m2 <- m[include_list, , drop = FALSE] 251.5875 256.4012 275.9379 263.2740 277.1073 459.7414   100   b
    m1 <- m[rownames(m) %in% include_list, , drop = FALSE] 226.1647 229.9530 239.3308 234.0090 239.8762 305.8925   100  a 
            m4 <- subset(m, rownames(m) %in% include_list) 227.7144 230.8488 242.3036 234.8678 239.1995 388.8809   100  a