Question

我有一个大文件〜100k行和100列，我想基于另一列创建提取四列的信息。有一个名为Caller的列，该列告诉您带有.sample的哪些列将包含noSample以外的信息。

我已经尝试过使用if and else if语句，但是有时会满足两个条件，并且编写所有可能的组合会花费很多精力，而且我很确定会有更好的方法

我的真实data.frame看起来像这样：

编辑

 Df <- data.frame(A = c("chr1", "chr1", "chr1", "chr1", "chr1", "chr1", "chr1"),
             B= c(10,12,13,14,15,16,17),
             Caller = c("A", "B", "C",  "D", "A,C", "A,B,C", "B,D"),
             A.sample = c("3xd|432", "noSample","noSample","noSample","1234|567|87sd","234|456|897a","noSample"),
             dummy1 = 1:7,
             B.sample = c("noSample", "456|789|asd", "noSample","noSample","noSample","674e|7892|123|432","bgcf|12er|567|zxs3|12ple"),
             dummy2 = 1:7,
             C.sample = c("noSample","noSample", "zxc|vbn|mn","noSample","gfd3|123|456|789","674e|7892|123","noSample" ),
             dummy3 = 1:7,
             D.sample = c("noSample","noSample", "noSample", "poi|uyh|gfrt|562", "noSample", "noSample", "567|zxs3|12ple"), stringsAsFactors=FALSE)

我想为每一行提取一个样本向量。这可以存储在列表或另一个R对象上。我将这些样本与每个样本与一个流程相关联的data.frame进行匹配。

  My desired output would be

  >row1
  3xd|432 
  >row2
   456|789|asd
  >row3
  zxc|vbn|mn
  >row4
  poi|uyh|gfrt|562
  >row5
  [1]1234|567|87sd [2]gfd3|123|456|789
  >row6
  [1]234|456|897a [2]674e|7892|123|432  [3]674e|7892|123
  >row7
  [1]bgcf|12er|567|zxs3|12ple  [2]567|zxs3|12ple

我想要的输出将不包括样本之间的管道|，但是我可以使用strsplit来消除它

由于data.frame很大，因此速度至关重要。

Answer 1

这是一个可能的解决方案：

Df <- data.frame(A = c("chr1", "chr1", "chr1", "chr1", "chr1", "chr1", "chr1"),
                 B= c(10,12,13,14,15,16,17),
                 Caller = c("A", "B", "C",  "D", "A,C", "A,B,C", "B,D"),
                 A.sample = c("3xd|432", "noSample","noSample","noSample","1234|567|87sd","234|456|897a","noSample"),
                 B.sample = c("noSample", "456|789|asd", "noSample","noSample","noSample","674e|7892|123|432","bgcf|12er|567|zxs3|12ple"),
                 C.sample = c("noSample","noSample", "zxc|vbn|mn","noSample","gfd3|123|456|789","674e|7892|123","noSample" ),
                 D.sample = c("noSample","noSample", "noSample", "poi|uyh|gfrt|562", "noSample", "noSample", "567|zxs3|12ple"),
                 stringsAsFactors=FALSE)

#find names of columns
names<-substr(names(Df), 1, 1)
#Set unwanted names to NA
names[-c(4:ncol(Df))]<-NA

#create a regular expression by replacing the comma with the or |
reg<-gsub(",", "\\|", Df$Caller)

#find the column matches
columns<-sapply(reg, function(x){grep(x, names)})    

#extract the desired columns out into a list
lapply(seq_along(columns), function(x){Df[x,columns[[x]]]})

我在数据框定义中添加了stringsAsFactors=FALSE，以便删除与因子级别相关的负担。

Answer 2

仅显示实现所需结果的多种可能方法之一。请注意，我使用与@ Dave2e相同的数据帧，即，我已将stringsAsFactors=F添加到对data.frame的调用中。

library(tidyverse)
out <- df %>% rowid_to_column() %>% # adding explicit row IDs
       gather(key, value, -rowid, -A, -B, -Caller) %>% # reshaping the dataframe
       filter(value != "noSample")

结果数据帧将如下所示：

out
   rowid    A  B Caller      key                    value
1      1 chr1 10      A A.sample                  3xd|432
2      5 chr1 15    A,C A.sample            1234|567|87sd
3      6 chr1 16  A,B,C A.sample             234|456|897a
4      2 chr1 12      B B.sample              456|789|asd
5      6 chr1 16  A,B,C B.sample        674e|7892|123|432
6      7 chr1 17    B,D B.sample bgcf|12er|567|zxs3|12ple
7      3 chr1 13      C C.sample               zxc|vbn|mn
8      5 chr1 15    A,C C.sample         gfd3|123|456|789
9      6 chr1 16  A,B,C C.sample            674e|7892|123
10     4 chr1 14      D D.sample         poi|uyh|gfrt|562
11     7 chr1 17    B,D D.sample           567|zxs3|12ple

现在，我们可以简单地子集化以获取所需结果：

out[out$rowid == 1,"value"]
[1] "3xd|432"
out[out$rowid == 5,"value"]
[1] "1234|567|87sd"    "gfd3|123|456|789"

根据data.frame r中另一列的值从一列中提取信息

2 个答案: