R help - Sep 2010 - average columns of data frame corresponding to replicates

Hi Group,

I have a data frame below. Within this data frame there are  samples
(columns) that are measured  more than once. Samples are indicated by
"idx". So "id1" is present in columns 1, 3, and 5. Not every
id is
repeated. I would like to create a new data frame so that the repeated
 ids are averaged. For example, in the new data frame, columns 1, 3,
and 5 of the original will be replaced by 1 new column  that is the
mean of these three. Thanks for any suggestions.

Juliet



myData <- data.frame("sample1.id1" =rep(1,10),
"sample1.id2"=rep(2,10),
"sample2.id1" = rep(2,10),
"sample1.id3" = 1:10,
"sample3.id1" = rep(1,10),
"sample1.id4" = 1:10,
"sample2.id2" = rep(1,10))

repeat_ids <- c("id1","id2")

try this:
> myData
   sample1.id1 sample1.id2 sample2.id1 sample1.id3 sample3.id1
sample1.id4 sample2.id2
1            1           2           2           1           1
  1           1
2            1           2           2           2           1
  2           1
3            1           2           2           3           1
  3           1
4            1           2           2           4           1
  4           1
5            1           2           2           5           1
  5           1
6            1           2           2           6           1
  6           1
7            1           2           2           7           1
  7           1
8            1           2           2           8           1
  8           1
9            1           2           2           9           1
  9           1
10           1           2           2          10           1
 10           1
> newData <- NULL
> for (i in repeat_ids){
+     # determine the columns to use
+     colIndx <- grep(paste(i, "$", sep=''),
colnames(myData))
+     if (length(colIndx) == 0) next  # make sure it exists
+     # create the average of the columns
+     newData <- cbind(newData, rowMeans(myData[, colIndx], na.rm=TRUE))
+     colnames(newData)[ncol(newData)] <- i  # add the name
+ }
> newData
           id1 id2
 [1,] 1.333333 1.5
 [2,] 1.333333 1.5
 [3,] 1.333333 1.5
 [4,] 1.333333 1.5
 [5,] 1.333333 1.5
 [6,] 1.333333 1.5
 [7,] 1.333333 1.5
 [8,] 1.333333 1.5
 [9,] 1.333333 1.5
[10,] 1.333333 1.5
>

On Tue, Sep 7, 2010 at 12:00 PM, Juliet Hannah <juliet.hannah at
gmail.com> wrote:
> Hi Group,
>
> I have a data frame below. Within this data frame there are ?samples
> (columns) that are measured ?more than once. Samples are indicated by
> "idx". So "id1" is present in columns 1, 3, and 5. Not
every id is
> repeated. I would like to create a new data frame so that the repeated
> ?ids are averaged. For example, in the new data frame, columns 1, 3,
> and 5 of the original will be replaced by 1 new column ?that is the
> mean of these three. Thanks for any suggestions.
>
> Juliet
>
>
>
> myData <- data.frame("sample1.id1" =rep(1,10),
> "sample1.id2"=rep(2,10),
> "sample2.id1" = rep(2,10),
> "sample1.id3" = 1:10,
> "sample3.id1" = rep(1,10),
> "sample1.id4" = 1:10,
> "sample2.id2" = rep(1,10))
>
> repeat_ids <- c("id1","id2")
>
> ______________________________________________
> 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.
>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

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