Re: [R] Help on read in a txt file

From: ss <affysnp_at_gmail.com>
Date: Thu, 24 Apr 2008 22:03:34 -0400

Thanks Jim.

I got this:

> A<-read.table("a.txt", sep="\t", fill=TRUE)
> dim(A)
[1] 33623 592
> x <- count.fields("a.txt", sep="\t")
which(x != 592) # print out the lines that are not correct
> which(x != 592) # print out the lines that are not correct
[1] 31279 31281 33625
>

Actually, I just need from the txt file to grab 83 columns whose column names have the pattern '_A01/Ratio'.

For instance, I am listing the column names of the first 23 columns and I only need
the columns ends with '_A01/Ratio'. So is there a way to get around reading in all
the data first?

Thanks,

       Alex

Database ebi.ac.uk:Database:ensembl
Database ebi.ac.uk:Database:locus
Database ebi.ac.uk:Database:refseq
Database ebi.ac.uk:Database:tigr_thc
Database www.chem.agilent.com:Database:agp
Reporter group
Reporter identifier
Reporter name
Reporter sequence type
MBA: US14702370_16012391010920_S01_A01/Log(Ratio)
MBA: US14702370_16012391010920_S01_A01/Ratio
MBA: US14702370_16012391010920_S01_A01/Fold Change
MBA: US14702370_16012391010920_S01_A01/Log(Error)
MBA: US14702370_16012391010920_S01_A01/P-Value
MBA: US14702370_16012391010920_S01_A01/Intensity 1
MBA: US14702370_16012391010920_S01_A01/Intensity 2
MBA: US14702370_16012391010525_S01_A01/Log(Ratio)
MBA: US14702370_16012391010525_S01_A01/Ratio
MBA: US14702370_16012391010525_S01_A01/Fold Change
MBA: US14702370_16012391010525_S01_A01/Log(Error)
MBA: US14702370_16012391010525_S01_A01/P-Value
MBA: US14702370_16012391010525_S01_A01/Intensity 1
MBA: US14702370_16012391010525_S01_A01/Intensity 2



On Thu, Apr 24, 2008 at 9:27 PM, jim holtman <jholtman_at_gmail.com> wrote:

> It seems to indicate that you don't have 592 columns on all lines.
> Try the following to see how many columns are in each line:
>
> x <- count.fields("A.txt", sep="\t")
> which(x != 592) # print out the lines that are not correct
>
> You might also try:
>
> read.table("a.txt", sep="\t", fill=TRUE)
>
> On Thu, Apr 24, 2008 at 8:32 PM, ss <affysnp_at_gmail.com> wrote:
> > Dear list,
> >
> > Hello! I had a problem of reading in a txt file and need your help.
> > The txt file, called A, comprises of 592 columns and 34179 rows.
> > I need to note that for some cells of A , A[i,j], are blank.
> >
> > I used read.table() and got the warning message:
> >
> > > A<-read.table(file="A.txt",sep="\t")
> > Warning message:
> > In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
> > number of items read is not a multiple of the number of columns
> > > dim(A)
> > [1] 33623 592
> >
> > However, as some rows were missed because the original number
> > of rows is 34179, after read.table(), it was decreased to 33623.
> > I have no idea whether it has anything to do with the warning message.
> >
> > Do you have any suggestions for this problem?
> >
> > Thanks much,
> > Alex
> >
> > [[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.
> >
>
>
>
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem you are trying to solve?
>

        [[alternative HTML version deleted]]



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