[R] Odp: read.table: fill=T for header?

From: Petr PIKAL <petr.pikal_at_precheza.cz>
Date: Wed, 27 Apr 2011 14:31:58 +0200

Hi

If I understand correctly you maybe could read a file without header, discard last column, read first line of a file and put it as column names.

read.delim(textConnection(infile), header=F, skip=1) scan(textConnection(infile), nlines=1, sep="\t", what=c("",""))

Regards
Petr

r-help-bounces_at_r-project.org napsal dne 27.04.2011 14:15:33:

>
> Dear ExpeRts,t
>
> I am trying to read tab delimted data produced by somewhat brain dead
> software that seems to think it's a good idea to have an extra tab
> character after the last column - except for the header line. As
> explained in the help page, read.delim now assumes that the first
> column contains the row.names (which is not even wrong) but now and all
> col.names get shiftet by one column. Example:
>
> infile <- 'sample\tx1\n1\tA\t\n2\tB\t\n3\tA\t'
> read.delim(textConnection(infile))
> sample x1
> 1 A NA
> 2 B NA
> 3 A NA
>
> So I set row.names to NULL because the man page said "Using
> ‘row.names = NULL’ forces row numbering.". Now the row.names really
> are numbered automatically but I get a "bonus column":
>
> read.delim(textConnection(infile), row.names=NULL)
> row.names sample x1
> 1 1 A NA
> 2 2 B NA
> 3 3 A NA
>
> Hm - not what I want. I am also a bit puzzeled why the extra column is
> introduced instead of just using the first col.name. At the moment I
> deal with it by fixing the col.names and dumping the extra column:
>
> dat <- read.delim(textConnection(infile), row.names=NULL)
> colnames(dat) <- colnames(dat)[-1]
> dat <- dat[-ncol(dat)]
> dat
> sample x1
> 1 1 A
> 2 2 B
> 3 3 A
>
> I worked my way through ?read.delim but could not find an option to
> deal with these (flawed) files directly. As the opposite situation
> (i.e. more col.names than data) can be fixed with fill=T I was hoping
> something like fill.header=T or fill='header' may exist. Did I just
> not find it or does it not exist? And if it doesn't - does anyone
> else think it would be a nice item for the wishlist?
>
> cu
> Philipp
>
>
> --
> Dr. Philipp Pagel
> Lehrstuhl für Genomorientierte Bioinformatik
> Technische Universität München
> Wissenschaftszentrum Weihenstephan
> Maximus-von-Imhof-Forum 3
> 85354 Freising, Germany
> http://webclu.bio.wzw.tum.de/~pagel/
>
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