Question

说我有下表：

数据

df1 <- structure(list(sample = c("WT_mock", "WT_mock", "WT_mock", "WT_stim", 
"WT_stim", "WT_mock", "WT_mock", "WT_mock", "WT_stim", "WT_stim"
), target = c("ref", "goi1", "goi2", "goi1", "goi2", "ref", "goi1", 
"goi2", "goi1", "goi2"), replicate = c(1L, 1L, 1L, 1L, 1L, 2L, 
2L, 2L, 2L, 2L), mean = c(15L, 20L, 21L, 22L, 23L, 15L, 20L, 
21L, 22L, 23L)), class = "data.frame", row.names = c("1", "2", 
"3", "4", "5", "6", "7", "8", "9", "10"))

# A tibble: 10 x 4
   sample  target replicate  mean
   <chr>   <chr>      <dbl> <dbl>
 1 WT_mock ref            1    15
 2 WT_mock goi1           1    20
 3 WT_mock goi2           1    21
 4 WT_stim goi1           1    22
 5 WT_stim goi2           1    23
 6 WT_mock ref            2    15
 7 WT_mock goi1           2    20
 8 WT_mock goi2           2    21
 9 WT_stim goi1           2    22
10 WT_stim goi2           2    23

我正在尝试从我的参考文献（WT_mock，ref）中减去每个goi的平均值，以创建此副本：

# A tibble: 10 x 5
   sample  target replicate  mean   dCt
   <chr>   <chr>      <dbl> <dbl> <dbl>
 1 WT_mock ref            1    15     0
 2 WT_mock goi1           1    20    -5
 3 WT_mock goi2           1    21    -6
 4 WT_stim goi1           1    22    -7
 5 WT_stim goi2           1    23    -8
 6 WT_mock ref            2    15     0
 7 WT_mock goi1           2    20    -5
 8 WT_mock goi2           2    21    -6
 9 WT_stim goi1           2    22    -7
10 WT_stim goi2           2    23    -8

我知道有几种生物导体封装可以做到这一点，但是我想以此作为练习使用R进行数据操作。

我的方法是每次复制filter并“手动”减去ref值，但是我想有一种更优雅的方法来解决此问题（dplyr等）我的真实数据集有多个重复样本，我想知道是否有更快的方法来实现这一目标。

非常感谢！

Answer 1

按“复制”分组后，通过从与“目标”中“参考”值相对应的平均值中减去“平均值”来创建“ dCt”

library(dplyr)
df1 %>%
    group_by(replicate) %>%
     mutate(dCt = mean[target == 'ref'] - mean)
# A tibble: 10 x 5
# Groups:   replicate [2]
#   sample  target replicate  mean   dCt
#   <chr>   <chr>      <int> <int> <int>
# 1 WT_mock ref            1    15     0
# 2 WT_mock goi1           1    20    -5
# 3 WT_mock goi2           1    21    -6
# 4 WT_stim goi1           1    22    -7
# 5 WT_stim goi2           1    23    -8
# 6 WT_mock ref            2    15     0
# 7 WT_mock goi1           2    20    -5
# 8 WT_mock goi2           2    21    -6
# 9 WT_stim goi1           2    22    -7
#10 WT_stim goi2           2    23    -8

或使用match

df1 %>% 
  group_by(replicate) %>%
  mutate(dCt = mean[match('ref', target)] - mean)

或使用data.table

library(data.table)
setDT(df1)[, dCt := mean[match('ref', target)] - mean, by = replicate]

在base R中，我们也可以这样做

df1$dCt <-  with(df1,  mean[target == 'ref'][replicate] - mean)

数据

df1 <- structure(list(sample = c("WT_mock", "WT_mock", "WT_mock", "WT_stim", 
"WT_stim", "WT_mock", "WT_mock", "WT_mock", "WT_stim", "WT_stim"
), target = c("ref", "goi1", "goi2", "goi1", "goi2", "ref", "goi1", 
"goi2", "goi1", "goi2"), replicate = c(1L, 1L, 1L, 1L, 1L, 2L, 
2L, 2L, 2L, 2L), mean = c(15L, 20L, 21L, 22L, 23L, 15L, 20L, 
21L, 22L, 23L)), class = "data.frame", row.names = c("1", "2", 
"3", "4", "5", "6", "7", "8", "9", "10"))

Answer 2

以下是一些基本的R解决方案：

如果始终将ref作为各个组的第一行，也许您可以尝试以下代码

df <- within(df,dCt<-ave(mean,replicate,FUN = function(x) head(x,1)-x))

否则（ref不是相应组中的第一行）

df <- do.call(rbind,c(make.row.names = FALSE,
                      lapply(split(df,df$replicate),
                             function(v) within(v,dCt<-mean[target=="ref"]-mean))))

以上两种都会给你

> df
    sample target replicate mean dCt
1  WT_mock    ref         1   15   0
2  WT_mock   goi1         1   20  -5
3  WT_mock   goi2         1   21  -6
4  WT_stim   goi1         1   22  -7
5  WT_stim   goi2         1   23  -8
6  WT_mock    ref         2   15   0
7  WT_mock   goi1         2   20  -5
8  WT_mock   goi2         2   21  -6
9  WT_stim   goi1         2   22  -7
10 WT_stim   goi2         2   23  -8

从匹配组中减去值

2 个答案:

数据