[R] how to emerge two tables by taking the ave.

[affy snp]

Hi Jim,

Thanks a lot! I am wondering why I ended up getting the result as follows:

> x<-read.table(file="x.txt",header=TRUE,row.names=1,na.strings = "NA")
Warning message:
In read.table(file = "x.txt", header = TRUE, row.names = 1, na.strings = "NA") :
  incomplete final line found by readTableHeader on 'x.txt'
> x
   b1 b2 b3
a1  2  4  6
a2  1  2 NA
a3  4  6 NA
> y<-as.matrix(read.table(file="y.txt",header=TRUE,row.names=1,na.strings = "NA"))
Warning message:
In read.table(file = "y.txt", header = TRUE, row.names = 1, na.strings = "NA") :
  incomplete final line found by readTableHeader on 'y.txt'
> y
   b1 b2 b3
a1 NA  4  4
a2  2  2 NA
a3  1  2  2
> z <- mapply(function(a,b)mean(c(a,b), na.rm=TRUE), x, y)
> z
      b1       b2       b3     <NA>     <NA>     <NA>     <NA>     <NA>
2.333333 3.500000 3.500000 2.750000 3.500000 4.000000 2.750000 4.000000
    <NA>
4.000000
> dim(z) <- dim(x)
> z
         [,1] [,2] [,3]
[1,] 2.333333 2.75 2.75
[2,] 3.500000 3.50 4.00
[3,] 3.500000 4.00 4.00
> is.na(z) <- is.nan(z)
> z
         [,1] [,2] [,3]
[1,] 2.333333 2.75 2.75
[2,] 3.500000 3.50 4.00
[3,] 3.500000 4.00 4.00
>


Allen

On Nov 11, 2007 5:27 PM, jim holtman <jholtman at gmail.com> wrote:
> Here is one way of doing it:
>
> > x
>      [,1] [,2] [,3]
> [1,]    2    4    6
> [2,]    1    2   NA
> [3,]    4    6   NA
> > y
>      [,1] [,2] [,3]
> [1,]   NA    4    4
> [2,]    2    2   NA
> [3,]    1    2    2
> > z <- mapply(function(a,b)mean(c(a,b), na.rm=TRUE), x, y)
> > dim(z) <- dim(x)
> > z
>      [,1] [,2] [,3]
> [1,]  2.0    4    5
> [2,]  1.5    2  NaN
> [3,]  2.5    4    2
> > # to change it to NA
> > is.na(z) <- is.nan(z)
> > z
>      [,1] [,2] [,3]
> [1,]  2.0    4    5
> [2,]  1.5    2   NA
> [3,]  2.5    4    2
>
> >
> >
>
>
> On Nov 11, 2007 4:52 PM, affy snp <affysnp at gmail.com> wrote:
> > Dear list,
> >
> > I am new to R and very inexperienced. Sorry for the trouble.
> > I have two txt files and want to merge them by taking the average.
> > More specifically, for example, the txt file1, with row names and column names,
> > consists of 238000 rows and 196 columns. Each column corresponds
> > to a sample. The data is mixed with numeric or NA. So what I plan to
> > do is:
> >
> > (1) Take the 1st column from txt file 1 and txt file 2, calculate the average
> > if both numbers are numeric. If one is numeric and the other one is NA or
> > the opposite, just use the numeric; If both are NA, then use NA, Do all this
> > for all columns
> > (2) Create txt file 3 with the numbers from the above and add the row names and
> > column names.
> >
> > So an illustrative example could be:
> >
> > txt file 1
> >
> >             A       B       C
> > row1      2       4        6
> > row2      1       2       NA
> > row3      4       6       NA
> >
> > txt file 2
> >
> >            A        B      C
> > row1     NA      4       4
> > row2     2         2      NA
> > row3     1         2      2
> >
> > then txt file 3 will be created as:
> >
> >            A        B       C
> > row1     2         4       5
> > row2    1.5       2       NA
> > row3    2.5       4       2
> >
> > Any help will be appreciated.
> >
> > Thanks!
> >       Allen
> >
> > ______________________________________________
> > 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
>
> What is the problem you are trying to solve?
>