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

[affy snp]

Hi,Jim. I created two txt files as:

x.txt

id b1   b2   b3
a1 2    4    6
a2 1    2   NA
a3 4    6   NA

y.txt
id    b1  b2  b3
a1  NA    4    4
a2  2    2   NA
a3  1    2    2


I tried it one more time but got different z:

> 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<-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)
> dim(z) <- dim(x)
Error in dim(z) <- dim(x) :
  dims [product 9] do not match the length of object [3]
> z <- mapply(function(a,b)mean(c(a,b), na.rm=TRUE), x, y)
> z
      b1       b2       b3
2.000000 3.333333 4.000000
>


Allen
On Nov 11, 2007 10:41 PM, jim holtman <jholtman at gmail.com> wrote:
> What did your text files look like?  It would appear that there was
> not a line feed on the last line of the file.  Also what does 'str' of
> x and y show?  It appears that one is a data frame and one is a
> matrix.  That might be causing some of the problems.
>
>
> On Nov 11, 2007 10:30 PM, affy snp <affysnp at gmail.com> wrote:
> > 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?
> > >
> >
>
>
>
> --
>
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem you are trying to solve?
>