thr3ads.net - R help - [R] Find and replace all the elements in a data frame [Feb 2011]

If this information is useful, please help other people find it:
Share via:

Josh B

2011-Feb-17 16:54 UTC

[R] Find and replace all the elements in a data frame

Hi all,

I'm having a problem once again, trying to do something very simple.
Consider
the following data frame:

x <- read.table(textConnection("locus1 locus2 locus3
A T C
A T NA
T C C
A T G"), header = TRUE)
closeAllConnections()

I am trying to make a new data frame, replacing "A" with
"A/A", "T" with "T/T",
"G" with "G/G", and "C" with "C/C." Note
also the presence of an "NA" (missing
data) in the data frame, which should be carried over to the new data frame.

Here is what I am trying, which fails miserably:

x2 <- data.frame(matrix(nrow = nrow(x), ncol = ncol(x)))

for (i in 1:nrow(x)){
    for (j in 1:ncol(x)){
        if(x[i, j] == 'A') {x2[i, j] <- 'A/A'} else{
            if(x[i, j] == 'T') {x2[i, j] <- 'T/T'} else{
                 if(x[i, j] == 'G') {x2[i, j] <- 'G/G'} else{
                    if(x[i, j] == 'G') {x2[i, j] <- 'G/G'}
else{x2[i, j] <- NA}
                }
           }
       }
    }
}

I get the following error message:
Error in if (x[i, j] == "A") { : missing value where TRUE/FALSE needed

So what am I doing wrong? If you can provide me with specific code that fixes 
the problem and gets the job done, that would be the most useful. 


Thanks very much in advance for your help!

Sincerely,
-----------------------------------
Josh Banta, Ph.D
Center for Genomics and Systems Biology
New York University
100 Washington Square East
New York, NY 10003
Tel: (212) 998-8465
http://plantevolutionaryecology.org


      
	[[alternative HTML version deleted]]

Henrique Dallazuanna

2011-Feb-17 17:22 UTC

head link

[R] Find and replace all the elements in a data frame

Try this:

xNew <- as.data.frame(mapply(paste, x, x, sep = "/"))
xNew[is.na(x)] <- NA
xNew

On Thu, Feb 17, 2011 at 2:54 PM, Josh B <joshb41@yahoo.com> wrote:
> Hi all,
>
> I'm having a problem once again, trying to do something very simple.
> Consider
> the following data frame:
>
> x <- read.table(textConnection("locus1 locus2 locus3
> A T C
> A T NA
> T C C
> A T G"), header = TRUE)
> closeAllConnections()
>
> I am trying to make a new data frame, replacing "A" with
"A/A", "T" with
> "T/T",
> "G" with "G/G", and "C" with "C/C."
Note also the presence of an "NA"
> (missing
> data) in the data frame, which should be carried over to the new data
> frame.
>
> Here is what I am trying, which fails miserably:
>
> x2 <- data.frame(matrix(nrow = nrow(x), ncol = ncol(x)))
>
> for (i in 1:nrow(x)){
>    for (j in 1:ncol(x)){
>        if(x[i, j] == 'A') {x2[i, j] <- 'A/A'} else{
>            if(x[i, j] == 'T') {x2[i, j] <- 'T/T'} else{
>                 if(x[i, j] == 'G') {x2[i, j] <- 'G/G'}
else{
>                    if(x[i, j] == 'G') {x2[i, j] <-
'G/G'} else{x2[i, j] <-
> NA}
>                }
>           }
>       }
>    }
> }
>
> I get the following error message:
> Error in if (x[i, j] == "A") { : missing value where TRUE/FALSE
needed
>
> So what am I doing wrong? If you can provide me with specific code that
> fixes
> the problem and gets the job done, that would be the most useful.
>
>
> Thanks very much in advance for your help!
>
> Sincerely,
> -----------------------------------
> Josh Banta, Ph.D
> Center for Genomics and Systems Biology
> New York University
> 100 Washington Square East
> New York, NY 10003
> Tel: (212) 998-8465
> http://plantevolutionaryecology.org
>
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O

	[[alternative HTML version deleted]]

Gong-Yi Liao

2011-Feb-17 17:24 UTC

head link

[R] Find and replace all the elements in a data frame

You may write as this:

for (i in 1:nrow(x)){
   for (j in 1:ncol(x)){
       if (!is.na(x[i, j])) {
          if(x[i, j] == 'A') {x2[i, j] <- 'A/A'} else{
              if(x[i, j] == 'T') {x2[i, j] <- 'T/T'} else{
                   if(x[i, j] == 'G') {x2[i, j] <- 'G/G'}
else{
                      if(x[i, j] == 'G') {x2[i, j] <- 'G/G'}
else{x2[i, j]
<- NA}
                 }
              }
          }
       }
   }
}


On Thu, Feb 17, 2011 at 11:54 AM, Josh B <joshb41@yahoo.com> wrote:
> Hi all,
>
> I'm having a problem once again, trying to do something very simple.
> Consider
> the following data frame:
>
> x <- read.table(textConnection("locus1 locus2 locus3
> A T C
> A T NA
> T C C
> A T G"), header = TRUE)
> closeAllConnections()
>
> I am trying to make a new data frame, replacing "A" with
"A/A", "T" with
> "T/T",
> "G" with "G/G", and "C" with "C/C."
Note also the presence of an "NA"
> (missing
> data) in the data frame, which should be carried over to the new data
> frame.
>
> Here is what I am trying, which fails miserably:
>
> x2 <- data.frame(matrix(nrow = nrow(x), ncol = ncol(x)))
>
> for (i in 1:nrow(x)){
>    for (j in 1:ncol(x)){
>        if(x[i, j] == 'A') {x2[i, j] <- 'A/A'} else{
>            if(x[i, j] == 'T') {x2[i, j] <- 'T/T'} else{
>                 if(x[i, j] == 'G') {x2[i, j] <- 'G/G'}
else{
>                    if(x[i, j] == 'G') {x2[i, j] <-
'G/G'} else{x2[i, j] <-
> NA}
>                }
>           }
>       }
>    }
> }
>
> I get the following error message:
> Error in if (x[i, j] == "A") { : missing value where TRUE/FALSE
needed
>
> So what am I doing wrong? If you can provide me with specific code that
> fixes
> the problem and gets the job done, that would be the most useful.
>
>
> Thanks very much in advance for your help!
>
> Sincerely,
> -----------------------------------
> Josh Banta, Ph.D
> Center for Genomics and Systems Biology
> New York University
> 100 Washington Square East
> New York, NY 10003
> Tel: (212) 998-8465
> http://plantevolutionaryecology.org
>
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Gong-Yi Liao

Department of Statistics
University of Connecticut
215 Glenbrook Road  U4120
Storrs, CT 06269-4120

860-486-9478

	[[alternative HTML version deleted]]

Sarah Goslee

2011-Feb-17 17:25 UTC

head link

[R] Find and replace all the elements in a data frame

Josh, you've made it far too complicated. Here's one simpler way (note
that I changed your read.table statement to make the values NOT factors,
since I wouldn't think you want that).
> x <- read.table(textConnection("locus1 locus2 locus3+ A T C
+ A T NA
+ T C C
+ A T G"), header = TRUE, as.is=TRUE)> closeAllConnections()
>
> x2 <- x
> x2[x2 == "A"] <- "A/A"
> x2[x2 == "T"] <- "T/T"
> x2[x2 == "G"] <- "G/G"
> x2[x2 == "C"] <- "C/C"
> x2  locus1 locus2 locus3
1    A/A    T/T    C/C
2    A/A    T/T   <NA>
3    T/T    C/C    C/C
4    A/A    T/T    G/G

If you do for some reason want a factor, you'll need to adjust the
levels for each
column before doing this.

Sarah

On Thu, Feb 17, 2011 at 11:54 AM, Josh B <joshb41 at yahoo.com>
wrote:> Hi all,
>
> I'm having a problem once again, trying to do something very simple.
Consider
> the following data frame:
>
> x <- read.table(textConnection("locus1 locus2 locus3
> A T C
> A T NA
> T C C
> A T G"), header = TRUE)
> closeAllConnections()
>
> I am trying to make a new data frame, replacing "A" with
"A/A", "T" with "T/T",
> "G" with "G/G", and "C" with "C/C."
Note also the presence of an "NA" (missing
> data) in the data frame, which should be carried over to the new data
frame.
>
> Here is what I am trying, which fails miserably:
>
> x2 <- data.frame(matrix(nrow = nrow(x), ncol = ncol(x)))
>
> for (i in 1:nrow(x)){
> ? ?for (j in 1:ncol(x)){
> ? ? ? ?if(x[i, j] == 'A') {x2[i, j] <- 'A/A'} else{
> ? ? ? ? ? ?if(x[i, j] == 'T') {x2[i, j] <- 'T/T'} else{
> ? ? ? ? ? ? ? ? if(x[i, j] == 'G') {x2[i, j] <- 'G/G'}
else{
> ? ? ? ? ? ? ? ? ? ?if(x[i, j] == 'G') {x2[i, j] <-
'G/G'} else{x2[i, j] <- NA}
> ? ? ? ? ? ? ? ?}
> ? ? ? ? ? }
> ? ? ? }
> ? ?}
> }
>
> I get the following error message:
> Error in if (x[i, j] == "A") { : missing value where TRUE/FALSE
needed
>
> So what am I doing wrong? If you can provide me with specific code that
fixes
> the problem and gets the job done, that would be the most useful.
>
>
> Thanks very much in advance for your help!
>
> Sincerely,
> -----------------------------------
> Josh Banta, Ph.D
> Center for Genomics and Systems Biology
> New York University
> 100 Washington Square East
> New York, NY 10003
> Tel: (212) 998-8465
> http://plantevolutionaryecology.org
>
>
>
> ? ? ? ?[[alternative HTML version deleted]]



-- 
Sarah Goslee
http://www.functionaldiversity.org

baptiste auguie

2011-Feb-17 17:29 UTC

head link

[R] Find and replace all the elements in a data frame

Hi,

You could use car::recode to change the levels of the factors,

library(car)
transform(x, locus1 = recode(locus1, "'A' = 'A/A' ; else =
'T/T'"),
                    locus2 = recode(locus2, "'T'='T/T' ;
'C' = 'C/C'"),
                    locus3 = recode(locus3, "'C'='C/C' ;
'G' = 'G/G'"))


HTH,

baptiste


On 17 February 2011 17:54, Josh B <joshb41 at yahoo.com>
wrote:> Hi all,
>
> I'm having a problem once again, trying to do something very simple.
Consider
> the following data frame:
>
> x <- read.table(textConnection("locus1 locus2 locus3
> A T C
> A T NA
> T C C
> A T G"), header = TRUE)
> closeAllConnections()
>
> I am trying to make a new data frame, replacing "A" with
"A/A", "T" with "T/T",
> "G" with "G/G", and "C" with "C/C."
Note also the presence of an "NA" (missing
> data) in the data frame, which should be carried over to the new data
frame.
>
> Here is what I am trying, which fails miserably:
>
> x2 <- data.frame(matrix(nrow = nrow(x), ncol = ncol(x)))
>
> for (i in 1:nrow(x)){
> ? ?for (j in 1:ncol(x)){
> ? ? ? ?if(x[i, j] == 'A') {x2[i, j] <- 'A/A'} else{
> ? ? ? ? ? ?if(x[i, j] == 'T') {x2[i, j] <- 'T/T'} else{
> ? ? ? ? ? ? ? ? if(x[i, j] == 'G') {x2[i, j] <- 'G/G'}
else{
> ? ? ? ? ? ? ? ? ? ?if(x[i, j] == 'G') {x2[i, j] <-
'G/G'} else{x2[i, j] <- NA}
> ? ? ? ? ? ? ? ?}
> ? ? ? ? ? }
> ? ? ? }
> ? ?}
> }
>
> I get the following error message:
> Error in if (x[i, j] == "A") { : missing value where TRUE/FALSE
needed
>
> So what am I doing wrong? If you can provide me with specific code that
fixes
> the problem and gets the job done, that would be the most useful.
>
>
> Thanks very much in advance for your help!
>
> Sincerely,
> -----------------------------------
> Josh Banta, Ph.D
> Center for Genomics and Systems Biology
> New York University
> 100 Washington Square East
> New York, NY 10003
> Tel: (212) 998-8465
> http://plantevolutionaryecology.org
>
>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Seemingly Similar Threads

Search for more possibly parallel threads

R help - Feb 2011 - Find and replace all the elements in a data frame

[R] Find and replace all the elements in a data frame

[R] Find and replace all the elements in a data frame

[R] Find and replace all the elements in a data frame

[R] Find and replace all the elements in a data frame

[R] Find and replace all the elements in a data frame

Seemingly Similar Threads