分布多个协调列

Question

我有相对整齐的数据，样本、基因、等位基因和频率分别位于不同的列中。对于每个基因和每个样本，我需要将等位基因及其相应的频率分成单独的列。这就是我拥有的和需要的。

尝试使用 dplyr/tidyr 执行此操作，但我会采取任何我能得到的解决方案。

我有什么：

data.frame(sample=rep("sample1", 10), 
           gene=rep(paste0("gene", 1:5), each=2), 
           allele=c("A", "G", "A", "C", "A", "T", "C", "G", "G", "T"), 
           freq=c(.9, .1, .8, .2, .7, .3, .6, .4, .5, .5))

#     sample  gene allele freq
# 1  sample1 gene1      A  0.9
# 2  sample1 gene1      G  0.1
# 3  sample1 gene2      A  0.8
# 4  sample1 gene2      C  0.2
# 5  sample1 gene3      A  0.7
# 6  sample1 gene3      T  0.3
# 7  sample1 gene4      C  0.6
# 8  sample1 gene4      G  0.4
# 9  sample1 gene5      G  0.5
# 10 sample1 gene5      T  0.5

我想要什么：

data.frame(sample=rep("sample1", 5), 
           gene=paste0("gene", 1:5), 
           allele1=c("A", "A", "A", "C", "G"), 
           allele2=c("G", "C", "T", "G", "T"), 
           freq1=c(.9, .8, .7, .6, .5), 
           freq2=c(.1, .2, .3, .4, .5))

#    sample  gene allele1 allele2 freq1 freq2
# 1 sample1 gene1       A       G   0.9   0.1
# 2 sample1 gene2       A       C   0.8   0.2
# 3 sample1 gene3       A       T   0.7   0.3
# 4 sample1 gene4       C       G   0.6   0.4
# 5 sample1 gene5       G       T   0.5   0.5

Answer 1

您可以使用data.tableie 的开发版本中的dcast。 1.9.5+ 可以采用多个 value.var 列。我们创建一个按“sample”和“gene”分组的序列列（“indx”）。然后dcast 从长格式到宽格式提到value.var 列。

 library(data.table)#v1.9.5+ 
 setDT(df)[, indx:=1:.N,.(sample, gene)]
 dcast(df, sample+gene~indx, value.var=c('allele', 'freq'), sep= '')
 #    sample  gene   allele1 allele2  freq1 freq2
 #1: sample1 gene1        A        G    0.9    0.1
 #2: sample1 gene2        A        C    0.8    0.2
 #3: sample1 gene3        A        T    0.7    0.3
 #4: sample1 gene4        C        G    0.6    0.4
 #5: sample1 gene5        G        T    0.5    0.5

注意：安装devel版本的说明是here

sep='' 参数对于将列名称创建为“allele1”、“allele2”等很有用。默认值为“allele_1”、“allele_2”等（来自@Arun 的 cmets）

Answer 2

这使用汇总而不是真正的重塑，但可能符合要求。

library(dplyr)
foo <- data.frame(sample=rep("sample1", 10), 
                  gene=rep(paste0("gene", 1:5), each=2), 
                  allele=c("A", "G", "A", "C", "A", "T", "C", "G", "G", "T"), 
                  freq=c(.9, .1, .8, .2, .7, .3, .6, .4, .5, .5))

foo %>%
  group_by(sample, gene) %>% 
  summarise(allele1 = first(allele), allele2 = last(allele),
            freq1 = first(freq), freq2 = last(freq))

## Source: local data frame [5 x 6]
## Groups: sample
## 
##    sample  gene allele1 allele2 freq1 freq2
## 1 sample1 gene1       A       G   0.9   0.1
## 2 sample1 gene2       A       C   0.8   0.2
## 3 sample1 gene3       A       T   0.7   0.3
## 4 sample1 gene4       C       G   0.6   0.4
## 5 sample1 gene5       G       T   0.5   0.5

Answer 3

您可以自行加入表格，然后选择适当的行。

library(dplyr)

table <- data.frame(sample=rep("sample1", 10), 
              gene=rep(paste0("gene", 1:5), each=2), 
              allele=c("A", "G", "A", "C", "A", "T", "C", "G", "G", "T"), 
              freq=c(.9, .1, .8, .2, .7, .3, .6, .4, .5, .5))

inner_join(table, table, by=c("sample","gene")) %>%
filter(allele.x != allele.y,
      (freq.x > freq.y | (freq.x == freq.y & as.numeric(allele.x) < as.numeric(allele.y))))

Answer 4

如果数据按样本和基因列排序，并且每个基因有 2 行，那么我们可以尝试如下：

cbind( df[ seq(1,nrow(df),2), ],
       df[ seq(2,nrow(df),2), -c(1,2) ] ) 

#output
#    sample  gene allele freq allele freq
# 1 sample1 gene1      A  0.9      G  0.1
# 3 sample1 gene2      A  0.8      C  0.2
# 5 sample1 gene3      A  0.7      T  0.3
# 7 sample1 gene4      C  0.6      G  0.4
# 9 sample1 gene5      G  0.5      T  0.5

Answer 5

我自己也在纠结这个问题。经典的重塑可以说是这里最清晰的？

df <- data.frame(sample=rep("sample1", 10), 
           gene=rep(paste0("gene", 1:5), each=2), 
           allele=c("A", "G", "A", "C", "A", "T", "C", "G", "G", "T"), 
           freq=c(.9, .1, .8, .2, .7, .3, .6, .4, .5, .5))

# make a time index
df$time = as.numeric( duplicated( df$gene ) ) # rep( c(1,2), nrow(df)/2 )
# reshape
reshape( df, idvar="gene", v.names=c("allele", "freq"), timevar="time", direction="wide")

但我真的很想从 tidyverse 得到一个干净的答案！