[英]How to pair rows in a data frame with many columns using dplyr in R?
我有一个数据框,其中包含来自对照和实验组的多个观察结果,每个受试者都有重复。
这是我的数据框的示例:
subject cohort replicate val1 val2
A control 1 10 0.1
A control 2 15 0.3
A experim 1 40 0.7
A experim 2 45 0.9
B control 1 5 0.3
B experim 1 30 0.0
C control 1 50 0.5
C experim 1 NA 1.0
我想将每个对照观察值与对应的实验观察值配对,以计算每个值之间的比率。 所需的输出如下所示:
subject replicate ratio_val1 ratio_val2
A 1 4 7
A 2 3 3
B 1 6 0
C 1 NA 2
理想情况下,我希望使用dplyr和管道实现此功能。
您可以使用summarize_at
功能从dplyr
总结列val1
和val2
通过分组数据后, subject
和replicate
。 使用[cohort == ...]
分别提取实验组和对照组的值进行划分:
library(dplyr)
df %>% group_by(subject, replicate) %>%
summarize_at(vars(contains('val')),
funs("ratio" = .[cohort == "experim"]/.[cohort == "control"]))
# Source: local data frame [4 x 4]
# Groups: subject [?]
#
# subject replicate val1_ratio val2_ratio
# <fctr> <int> <dbl> <dbl>
# 1 A 1 4 7
# 2 A 2 3 3
# 3 B 1 6 0
# 4 C 1 NA 2
我们可以通过将数据集重塑为“宽”格式来使用data.table
。
library(data.table)
dcast(setDT(df1), subject+replicate~cohort, value.var = c("val1", "val2"))[,
paste0("ratio_", names(df1)[4:5]) := Map(`/`, .SD[,
grep("experim", names(.SD)), with = FALSE],
.SD [, grep("control", names(.SD)), with = FALSE])][, (3:6) := NULL][]
# subject replicate ratio_val1 ratio_val2
# 1: A 1 4 7
# 2: A 2 3 3
# 3: B 1 6 0
# 4: C 1 NA 2
或在与“主题”,“复制”分组之后,我们遍历“ val”列,并将“ experim”的“ val”对应元素与“ control”的对应元素分开
setDT(df1)[, lapply(.SD[, grep("val", names(.SD)), with = FALSE],
function(x) x[cohort =="experim"]/x[cohort =="control"]) ,
by = .(subject, replicate)]
或者我们可以使用tidyr
gather/spread
library(dplyr)
library(tidyr)
df1 %>%
gather(Var, Val, val1:val2) %>%
spread(cohort, Val) %>%
group_by(subject, replicate, Var) %>%
summarise(ratio = experim/control) %>% spread(Var, ratio)
# subject replicate val1 val2
# <chr> <int> <dbl> <dbl>
# 1 A 1 4 7
# 2 A 2 3 3
# 3 B 1 6 0
# 4 C 1 NA 2
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