操作每个实验有多个列的数据框 [英] Manipulate a data frame where there are multiple colums for each experiment
问题描述
col2 <-C（Experiment1 1，a，b，c，d）
col3 <-C（Experiment1，Part 2，e，f，g h）
col4 < - c（Experiment2，Part 1，i，j，k，l）
col5< - c（Experiment2 part 2，m，n，o，p）
pp< - data.frame（col1，col2，col3，col4，col5）
one& 。框架（pp $ col1，pp $ col2）
onetwo< - data.frame（pp $ col1，pp $ col3）
two< -data.frame（pp $ col1，pp $ col4）
twotwo< -data.frame（pp $ col1，pp $ col5）
one $ V3 [3：6]< -as.character（one [2,2]）
one< -one [-2，]
one< --one [-1，]
colnames（1）< - c（gene，Experiment 1，part
onetwo $ V3 [3：6]< -as.character（onetwo [2,2]）
onetwo< -onetwo [-2，]
onetwo< onetwo [-1，]
colnames（onetwo）< - c（gene，Experiment 1，part）
x1 <-rbind（one，onetwo）
two $ V3 [3：6]< -as.character（two [2,2]）
two< -two [-2，]
two< -two [-1，]
colnames （2）< - c（基因，实验2，部分）
twotwo $ V3 [3：6]< -as.character（twotwo [ 2,2]）
twotwo <-twotwo [-2，]
twotwo <-twotwo [-1，]
colnames（twotwo）< - c（基因，实验2，part）
x2 <-rbind（two，twotwo）
x3 <-merge（x1，x2）
对于大量的代码，我深表歉意，但我无法具体说明此操作。 pp是示例数据帧，x3是我需要的格式。有没有更好的方法来实现？
这可能是一个较短的方法：
pp.new< - as.data.frame（t（pp）[ - 1，]，row.names = 1）
名称（pp.new）< - c（实验，部分，基因1，基因2，基因3，基因4）
其中：
> pp.new
实验部分gene1 gene2 gene3 gene4
1实验1第1部分abcd
2实验1第2部分efgh
3实验2第1部分ijkl
4实验2第2部分mnop
然而，使用 reshape2 将其转换为长格式可能更好package：
library（reshape2）
pp.long< - melt（pp.new，id = c 实验，部分））
导致：
> pp.long
实验部分变量值
1实验1第1部分基因1 a
2实验1第2部分基因1 e
3实验2第1部分gene1 i
4实验2第2部分基因1 m
5实验1第1部分基因2 b
6实验1第2部分基因2 f
7实验2第1部分基因2 j
8实验2第2部分基因2 n
9实验1第1部分基因3 c
10实验1第2部分基因3 g
11实验2第1部分gene3 k
12实验2第2部分基因3 o
13实验1第1部分gene4 d
14实验1第2部分gene4 h
15 Experiment2 Part 1 gene4 l
16 Experiment2 Part 2 gene4 p
如果要在 x3 中获得可比较的输出，可以使用 recast 函数（也可以从 reshape2 包）：
recast（pp.new，part + variable〜experiment，id.var = c （实验 ，part），value.var =value）
其中给出：
部分变量实验1实验2
1第1部分gene1 ai
2第1部分gene2 bj
3第1部分gene3 ck
4 Part 1 gene4 dl
5 Part 2 gene1 em
6 Part 2 gene2 fn
7 Part 2 gene3 go
8 Part 2 gene4 hp
I have many sequencing experiments each with multiple results for each of a few hundred genes, when the data is outputted from another programme it isn't in a useful format for me as all the Experiments and each result are listed along the top and there is one row for each gene. I have written an example data set and how I am currently solving this problem as an example but I would like a more optimal method as my data sets are very large.
col1<- c("","", "gene1", "gene2", "gene3", "gene4")
col2<- c("Experiment1", "Part 1", "a","b","c","d")
col3<- c("Experiment1", "Part 2", "e", "f", "g", "h")
col4<- c("Experiment2", "Part 1", "i", "j", "k", "l")
col5<- c("Experiment2", "Part 2", "m", "n", "o", "p")
pp<- data.frame(col1,col2,col3,col4,col5)
one<-data.frame(pp$col1, pp$col2)
onetwo<- data.frame(pp$col1,pp$col3)
two<-data.frame(pp$col1, pp$col4)
twotwo<-data.frame(pp$col1,pp$col5)
one$V3[3:6]<-as.character(one[2,2])
one<-one[-2,]
one<-one[-1,]
colnames(one)<- c("gene", "Experiment 1", "part")
onetwo$V3[3:6]<-as.character(onetwo[2,2])
onetwo<-onetwo[-2,]
onetwo<-onetwo[-1,]
colnames(onetwo)<- c("gene", "Experiment 1", "part")
x1<-rbind(one, onetwo)
two$V3[3:6]<-as.character(two[2,2])
two<-two[-2,]
two<-two[-1,]
colnames(two)<- c("gene", "Experiment 2", "part")
twotwo$V3[3:6]<-as.character(twotwo[2,2])
twotwo<-twotwo[-2,]
twotwo<-twotwo[-1,]
colnames(twotwo)<- c("gene", "Experiment 2", "part")
x2<-rbind(two, twotwo)
x3<-merge(x1,x2)
I apologise for the large amount of code but I am unable to verbalise this operation specifically. pp is the example data frame and x3 is the format I require. Is there a better way to do this?
This might be a shorter way to do it:
pp.new <- as.data.frame(t(pp)[-1,], row.names = 1)
names(pp.new) <- c("experiment", "part", "gene1", "gene2", "gene3", "gene4")
which gives:
> pp.new
experiment part gene1 gene2 gene3 gene4
1 Experiment1 Part 1 a b c d
2 Experiment1 Part 2 e f g h
3 Experiment2 Part 1 i j k l
4 Experiment2 Part 2 m n o p
However, it is probably better to transform this into long format with the reshape2 package:
library(reshape2)
pp.long <- melt(pp.new, id=c("experiment","part"))
which results in:
> pp.long
experiment part variable value
1 Experiment1 Part 1 gene1 a
2 Experiment1 Part 2 gene1 e
3 Experiment2 Part 1 gene1 i
4 Experiment2 Part 2 gene1 m
5 Experiment1 Part 1 gene2 b
6 Experiment1 Part 2 gene2 f
7 Experiment2 Part 1 gene2 j
8 Experiment2 Part 2 gene2 n
9 Experiment1 Part 1 gene3 c
10 Experiment1 Part 2 gene3 g
11 Experiment2 Part 1 gene3 k
12 Experiment2 Part 2 gene3 o
13 Experiment1 Part 1 gene4 d
14 Experiment1 Part 2 gene4 h
15 Experiment2 Part 1 gene4 l
16 Experiment2 Part 2 gene4 p
If you want to get a compareable output as in x3, you can use the recast function (also from the reshape2 package):
recast(pp.new, part + variable ~ experiment, id.var=c("experiment","part"), value.var = "value")
which gives:
part variable Experiment1 Experiment2
1 Part 1 gene1 a i
2 Part 1 gene2 b j
3 Part 1 gene3 c k
4 Part 1 gene4 d l
5 Part 2 gene1 e m
6 Part 2 gene2 f n
7 Part 2 gene3 g o
8 Part 2 gene4 h p
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