在具有不均匀数据帧的R中创建二进制矩阵

Question

我有一个包含8个不同组的microRNA的数据集。我需要使用R将数据框转换为二进制矩阵。microRNA的数量在组中有所不同，我想在行中创建组，并在列中使用microRNA。这是部分数据：

Group1    Group2    Group3   Group4
miR-133a  miR-133b  miR-456  miR777
miR-777   miR138    miR-564  miR-878
miR-878             miR-777  miR978
                    miR-878
                    miR-978

预期输出：

Groups  miR-133a  miR-133b  miR-456  miR-777.....
Group1  1             0      0        1
Group2  0             1      0        0
.
.
.

我尝试使用此代码：

im <- which(arr.ind=T,Dat!='');
u <- unique(Dat[im[order(im[,'row'],im[,'col']),]]);
res <- matrix(0L,nrow(Dat),length(u),dimnames=list(NULL,u));
res[cbind(im[,'row'],match(Dat[im],u))] <- 1L;
res

但是它给了我很多行。有人可以帮我吗？

Answer 1

这里是tidyverse的一个选项。重塑为“长”格式，然后使用pivot_wider

将其转换回“宽”格式

library(dplyr)
library(tidyr)
df1 %>%
    pivot_longer(cols = everything(), names_to = 'Groups', 
         values_drop_na = TRUE) %>%
    distinct %>%
    mutate(new =1) %>% 
    pivot_wider(names_from =value, values_from = new,  
           values_fill = list(new = 0))
#Groups `miR-133a` `miR-133b` `miR-456` miR777 `miR-777` miR138 `miR-564` `miR-878` miR978 `miR-978`
#  <chr>       <dbl>      <dbl>     <dbl>  <dbl>     <dbl>  <dbl>     <dbl>     <dbl>  <dbl>     <dbl>
#1 Group1          1          0         0      0         1      0         0         1      0         0
#2 Group2          0          1         0      0         0      1         0         0      0         0
#3 Group3          0          0         1      0         1      0         1         1      0         1
#4 Group4          0          0         0      1         0      0         0         1      1         0

---

或在base R中加上table

table(names(df1)[col(df1)], unlist(df1))
#           miR-133a miR-133b miR-456 miR-564 miR-777 miR-878 miR-978 miR138 miR777 miR978
#  Group1        1        0       0       0       1       1       0      0      0      0
#  Group2        0        1       0       0       0       0       0      1      0      0
#  Group3        0        0       1       1       1       1       1      0      0      0
#  Group4        0        0       0       0       0       1       0      0      1      1

注意：在这里，我们假设空白为NA。如果是""，请先将其更改为NA，然后使用相同的代码

df1[df1 == ""] <- NA

数据

df1 <- structure(list(Group1 = c("miR-133a", "miR-777", "miR-878", NA, 
NA), Group2 = c("miR-133b", "miR138", NA, NA, NA), Group3 = c("miR-456", 
"miR-564", "miR-777", "miR-878", "miR-978"), Group4 = c("miR777", 
"miR-878", "miR978", NA, NA)), class = "data.frame", row.names = c(NA, 
-5L))

Answer 2

假设数据框中的空格为“”：

df = structure(list(Group1 = c("miR-133a", "miR-777", "miR-878", "", 
""), Group2 = c("miR-133b", "miR138", "", "", ""), Group3 = c("miR-456", 
"miR-564", "miR-777", "miR-878", "miR-978"), Group4 = c("miR777", 
"miR-878", "miR978", "", "")), row.names = c(NA, -5L), class = "data.frame")

然后，对所有项目进行主设置：

alla = setdiff(sort(unique(unlist(df))),"")
res = t(sapply(colnames(df),function(i)as.numeric(alla %in% df[,i])))
colnames(res) = alla

       miR-133a miR-133b miR-456 miR-564 miR-777 miR-878 miR-978 miR138 miR777
Group1        1        0       0       0       1       1       0      0      0
Group2        0        1       0       0       0       0       0      1      0
Group3        0        0       1       1       1       1       1      0      0
Group4        0        0       0       0       0       1       0      0      1
       miR978
Group1      0
Group2      0
Group3      0
Group4      1