r - 如何根据阈值计算每一列中的行

Question

我有以下数据集:

dat <- structure(list(Probes = structure(1:6, .Label = c("1415670_at",
"1415671_at", "1415672_at", "1415673_at", "1415674_a_at", "1415675_at"
), class = "factor"), Genes = structure(c(2L, 1L, 4L, 5L, 6L,
3L), .Label = c("Atp6v0d1", "Copg1", "Dpm2", "Golga7", "Psph",
"Trappc4"), class = "factor"), bCD.ID.LN = c(1.133, 1.068, 1.01,
0.943, 1.048, 1.053), bCD.ID.LV = c(1.049, 1.006, 0.883, 0.799,
0.96, 1.104), bCD.ID.SP = c(1.124, 1.234, 1.029, 1.064, 1.118,
1.057), bCD.IP.LV = c(1.013, 1.082, 1.061, 0.982, 1.191, 1.053
), bCD.IP.SP = c(0.986, 1.102, 1.085, 0.997, 1.141, 1.041)), .Names = c("Probes",
"Genes", "bCD.ID.LN", "bCD.ID.LV", "bCD.ID.SP", "bCD.IP.LV",
"bCD.IP.SP"), row.names = c(NA, 6L), class = "data.frame")

看起来像这样:

> dat

        Probes    Genes bCD.ID.LN bCD.ID.LV bCD.ID.SP bCD.IP.LV bCD.IP.SP
1   1415670_at    Copg1     1.133     1.049     1.124     1.013     0.986
2   1415671_at Atp6v0d1     1.068     1.006     1.234     1.082     1.102
3   1415672_at   Golga7     1.010     0.883     1.029     1.061     1.085
4   1415673_at     Psph     0.943     0.799     1.064     0.982     0.997
5 1415674_a_at  Trappc4     1.048     0.960     1.118     1.191     1.141
6   1415675_at     Dpm2     1.053     1.104     1.057     1.053     1.041

我想要为第 3 列向前计数行添加值 > 1.1 的内容所以它最终看起来像这样:

bCD.ID.LN 1
bCD.ID.LV 1
bCD.ID.SP 3
bCD.IP.LV 1
bCD.IP.SP 2

我该怎么做？

Answer 1

我们可以在基于数据集中数字列的逻辑矩阵上尝试 colSums。

Count <- colSums(dat[-(1:2)] > 1.1, na.rm=TRUE)

如果我们需要它作为data.frame

d1 <- data.frame(Cnames = names(Count), Count=unname(Count))   

---

如果是大数据集，转换为逻辑矩阵可能内存效率不高，在这种情况下，最好使用 vapply 循环

vapply(dat[-(1:2)], function(x) sum(x > 1.1, na.rm=TRUE), 0)