replace value of each rows with value of column?

Question

I have a table like as below. I like to replace each sample value base on comparing with third first columns and code each value with(0,1,2,3). For example, if sample value in each row = REF_REF -> 1 ; if sample value in each row = REF_ALT -> 2 ; if sample value in each row = ALT_ALT -> 3 and for 0/0 -> 0.

REF_REF   REF_ALT   ALT_ALT       sample1       sample2     sample3

 A/A         A/G     G/G             0/0          A/G          G/G

T/T          T/C     C/C             T/T          T/C          T/C

C/C          C/G    G/G              0/0          C/G          C/G

I like to make a table like as:

REF_REF   REF_ALT   ALT_ALT       sample1       sample2     sample3

A/A         A/G       G/G           0               2           3

T/T         T/C       C/C           1               2           2

C/C        C/G       G/G            0               2           2

Also, I used this command but not work.

l=c()

for (i in seq_along(data))

{
 data=data[1,]

 Ref_Ref=data$Ref_Ref

 Alt_Alt=data$Ref_Ref

 Ref_Alt=data$Ref_Alt

 with( data[], ifelse( data == Ref_Ref, 1, ifelse(data == Alt_Alt, 3, 
if((data==Ref_Alt) 2))))

 if(data=Ref_Ref, data=1)

l[1,]=if(data==Ref_Ref, 1)

  l[1] <- if (data %in% data$Ref_Ref) 1 else if (data %in% data$Alt_Alt) 3  else if (data %in% data$Alt_Alt) 2 else 0  
}

l=c() for (i in seq_along(data)) { data=data[1,] Ref_Ref=data$Ref_Ref Alt_Alt=data$Ref_Ref Ref_Alt=data$Ref_Alt with( data[], ifelse( data == Ref_Ref, 1, ifelse(data == Alt_Alt, 3, if((data==Ref_Alt) 2)))) if(data=Ref_Ref, data=1) l[1,]=if(data==Ref_Ref, 1) l[1] <- if (data %in% data$Ref_Ref) 1 else if (data %in% data$Alt_Alt) 3 else if (data %in% data$Alt_Alt) 2 else 0 } — star
– star, Commented Dec 16, 2015 at 15:33
Can you put that in the question please? Don't put extra information in comments. — Heroka
– Heroka, Commented Dec 16, 2015 at 15:34

Heroka · Accepted Answer · 2015-12-16 16:03:58Z

2

This might work for you. It splits your data by row, and uses the useful properties of factors in R. For each row, we create a factor out of the samples, with levels of 0/0 followed by ref_ref, ref_alt and alt_alt. Then we convert this factor to numeric, and substract 1 to get the desired output.

recoded_samples <- apply(dat,1,function(x) {
  res <- as.numeric(factor(x[4:6],levels = c("0/0",x[1:3]))) - 1
  res
})

Then we can copy dat to an outcome variable (I don't like overwriting variables), and replace the columns. Note that we need to transpose 'res'.

outcome <- dat
outcome[,4:6] <- t(res)

> outcome
  REF_REF REF_ALT ALT_ALT sample1 sample2 sample3
1     A/A     A/G     G/G       0       2       3
2     T/T     T/C     C/C       1       2       2
3     C/C     C/G     G/G       0       2       2

edited Dec 16, 2015 at 16:03

answered Dec 16, 2015 at 15:47

Heroka

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Ven Yao · Accepted Answer · 2015-12-16 17:33:31Z

0

A dummy approach.

text1 <- "REF_REF   REF_ALT   ALT_ALT       sample1       sample2     sample3
A/A         A/G     G/G             0/0          A/G          G/G
T/T          T/C     C/C             T/T          T/C          T/C
C/C          C/G    G/G              0/0          C/G          C/G"

df <- read.table(text=text1, head=T, as.is=T)

for (x in 4:ncol(df)) {
  df[,x][df[,x]=="0/0"] <- 0
  df[,x][df[,x]==df[,1]] <- 1
  df[,x][df[,x]==df[,2]] <- 2
  df[,x][df[,x]==df[,3]] <- 3
}
# change characters to integers
df[,4:6] <- as.integer(as.matrix(df[, 4:6]))
df

edited Dec 16, 2015 at 17:33

answered Dec 16, 2015 at 17:26

Ven Yao

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2 Comments

Heroka Over a year ago

Won't this convert the numbers to character?

Ven Yao Over a year ago

Yes. @Heroka But I think it's okay as characters. And we can change character to integers if needed.

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