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How to replace number in R

How I can replace number in R 1 to11, 2 to 22 and 0 to 10, also -9 as NA?

         id        rs143        rs148       rs149      rs1490 
 1    02003s         -9          1          2          1    
 2    02003s         -9          0          1          2  
 3    02003s         -9          1          1          2   
 4    02003s         -9          0          1          1
 5    02003s         -9          0          1          1

I want to replace numbers as this format:

         id        rs143        rs148       rs149      rs1490 
 1    02003s         NA          11          22          11    
 2    02003s         NA          10          11          22   
 3    02003s         NA          11          11          22
 4    02003s         NA          10          11          11 
 5    02003s         NA          10          11          11

I tried this

  df[df==1]<-11
  df[df==2]<-22
  df[df==0]<-10

But this error occur:

 In [<-.factor`(`*tmp*`, thisvar, value = 22) :
 invalid factor level, NA generated
r replace number
• 10,337 views • link
updated by zx8754 zx8754 • written by Kian • Kian

check str of dataframe. I guess some of them are factors instead of integers.

• 1 views • link
written by cpad0112 cpad0112

Thank you cpda0112 and Dear Kevin for responses, how i can solve this problem!

• 1 views • link
written by Kian • Kian

can you paste output from str(head(df)), here?

• 1 views • link
written by cpad0112 cpad0112

1 answer

As mentioned in the comments some of the columns are class of factor, not numeric. If all SNP columns are numeric, then your existing code should work.

Try below code to convert, factor and numeric columns into numeric:

# lookup for allele recoding
lookup <- setNames(c(NA, 10, 11, 22), c(-9, 0, 1, 2))


res <- cbind(df[, 1, drop = FALSE], 
             data.frame(lapply(df[, -1], function(i) lookup[ as.character(i) ])))

res
#       id rs143 rs148 rs149 rs1490
# 1 02003s    NA    11    22     11
# 2 02003s    NA    10    11     22
# 3 02003s    NA    11    11     22
# 4 02003s    NA    10    11     11
# 5 02003s    NA    10    11     11
• 1 views • link
written by zx8754 zx8754

Thank you zx8754, its RIGHT!

• 1 views • link
written by Kian • Kian

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