Complement genotype

Question

[BlackHole]

I am beginner in R, so apologize for such a simple question

I have two columns

V1 V2
 T  1
 C  0
 A  1

if the column V2 is 1, then I want to replace nucleotide complementary if 0 is left as is I wrote a for functiom (in my many rows of data), but after his performance I get

V1 V2 V3
 T  1 NA
 C  0 NA
 A  1 T

And i want get

 V1 V2 V3
 T  1 T
 C  0 C
 A  1 T

where is the mistake?

whether it is possible to do it without the for, for examle using apply?

[WouterDeCoster]

Not really a bioinformatics question, might get closed. Which command did you try?

[BlackHole]

i try to use

  for(i in nrow(Tri1_a)){

     if(Tri1_a$V2[i] == 1){
      if(Tri1_a$V1[i] == "T")
        Tri1_a$V3[i] = "A"
      if(Tri1_a$V1[i] == "A")
        Tri1_a$V3[i] = "T"
      if(Tri1_a$V1[i] == "G")
        Tri1_a$V3[i] = "C"
      if(Tri1_a$V1[i] == "C")
        Tri1_a$V3[i] = "G"
    }
    else{
      Tri1_a$V3[i] = Tri1_a$V1[i]
    }

    i = i + 1
  }

[WouterDeCoster]

There probably is a better way... Why the i = i + 1? Could you edit your first post to contain the output you would like to obtain?

Answer 1

[ddiez]

Unless I am misunderstanding something, I thing what you want is:

# sample dataset (note the stringsAsFactors = FALSE).
Tri1_a <- data.frame(
  V1 = c("T", "C", "A"),
  V2 = c(1, 0, 1),
  V3 = c(NA, NA, "T"),
  stringsAsFactors = FALSE
)
Tri1_a
  V1 V2   V3
1  T  1 <NA>
2  C  0 <NA>
3  A  1    T

# replace NAs in V3 by the values at V1.
sel.na <- is.na(Tri1_a$V3)
Tri1_a$V3[sel.na] <- Tri1_a$V1[sel.na]
Tri1_a
  V1 V2 V3
1  T  1  T
2  C  0  C
3  A  1  T

Make sure your sequence data are not factors (you can probably pass stringsAsFactors = FALSE to the reading function, like read.table), or you might get an error saying:

Warning message:
In `[<-.factor`(`*tmp*`, sel.na, value = c(1L, NA, 1L)) :
  invalid factor level, NA generated

And the result will not be as expected.