CODEWITHSUNDEEP
rdataframe
user2380782
user2380782

Reputation: 1446

extract info from a column based on value from another column in data.frame r

I have a big file ~100k rows and 100 columns and I want to create extract the information of four columns based on another column. There is a column named Caller and that column tell you which columns with .sample will have info other than noSample.

I have tried with if and else if statements but sometimes two conditions are met and writting all the possible combinations would take a lot of effort and I am pretty sure there is a better way of doing it

My real data.frame looks like this one:

EDIT

 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)

I want to extract for each one of the rows a vector of samples. This could be stored on a list or another R object. I will use these samples to be matched against a data.frame where each sample is associated with a process.

  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

My desired output wouldn't include the pipe | between samples but I can get rid of it using strsplit

Since the data.frame is big the speed would be essential.

Upvotes: 2

Views: 1577

Answers (2)

Dave2e
Dave2e

Reputation: 24139

Here is a possible solution:

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]]]})

I added stringsAsFactors=FALSE to the data frame definition in order to remove the baggage related to the Factor levels.

Upvotes: 2

coffeinjunky
coffeinjunky

Reputation: 11514

Showing just one of many possible ways to achieve the desired result. Note that I use the same dataframe as @Dave2e, i.e. I have added stringsAsFactors=F to the call to data.frame.

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

The resulting dataframe will look like this:

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

Now we can simply subset to retrieve the desired result:

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

Upvotes: 2

Related Questions