根据两列获取频率

Question

我的大型数据框的片段看起来是这样的：

MARKERS.IN.HAPLOTYPES BASE           rs. alleles chrom       pos        GID marker   trial
                 1A.12    C S1A_494392059     C/G    1A 494392059 GID7173723      2 ES26-38
                 1A.13    C S1A_497201550     C/T    1A 497201550 GID7173723      0 ES26-38
                 1A.14    T S1A_499864157     C/T    1A 499864157 GID7173723      2 ES26-38
                 1B.10    A S1B_566171302     G/A    1B 566171302 GID7173723      0 ES26-38
                 1B.20    G S1B_642616640     A/G    1B 642616640 GID7173723      2 ES26-38
                 2B.10    A  S2B_24883552     A/G    2B  24883552 GID7173723      2 ES26-38

这是其中的一个dput：

structure(list(MARKERS.IN.HAPLOTYPES = c("1A.12", "1A.13", "1A.14", 
"1B.10", "1B.20", "2B.10"), BASE = c("C", "C", "T", "A", "G", 
"A"), rs. = c("S1A_494392059", "S1A_497201550", "S1A_499864157", 
"S1B_566171302", "S1B_642616640", "S2B_24883552"), alleles = c("C/G", 
"C/T", "C/T", "G/A", "A/G", "A/G"), chrom = c("1A", "1A", "1A", 
"1B", "1B", "2B"), pos = c(494392059L, 497201550L, 499864157L, 
566171302L, 642616640L, 24883552L), GID = c("GID7173723", "GID7173723", 
"GID7173723", "GID7173723", "GID7173723", "GID7173723"), marker = c("2", 
 "0", "2", "0", "2", "2"), trial = c("ES26-38", "ES26-38", "ES26-38", 
 "ES26-38", "ES26-38", "ES26-38")), row.names = c(NA, 6L), class = 
 "data.frame")

原始数据框中 rs. 列有 22 个 unique 值，trial 列有六个 unique 值。我想计算每个唯一 rs. 和每个唯一 trial 列 marker 不同值的相对频率。因此，例如，列 rs. S1A_494392059 的第一项将具有列 marker 用于试验的频率 ES26-38 等等，依此类推。请注意，marker 列是字符向量而不是数字。

Answer 1

你可以试试这个：

library(dplyr)

df %>%
  add_count(rs., trial, name = "Total") %>%
  add_count(rs., trial, marker, name = "MarkerTotal") %>%
  mutate(RelativeFreq = round(MarkerTotal / Total, 2))

add_count 中的 name 列是 dplyr 0.8 之后的新功能，允许您决定名称（以前是 n 或 nn 默认）。如果您没有更新包，上述代码将无法运行。

虽然不是特别复杂，但您示例中的相对频率到处都是 1。

如果您想获得汇总数据框（其中唯一剩下的列将分组 rs.、trial 和 RelativeFreq），您可以这样做：

df %>% 
  add_count(rs., trial, marker, name = "MarkerTotal") %>%
  group_by(rs., trial) %>%
  summarise(RelativeFreq = round(MarkerTotal / n(), 2))

根据两列获取频率

get frequency based on two columns

r

dplyr

tibble