[R] R error- "more columns than column names"

[David Winsemius]

On Feb 24, 2010, at 7:07 PM, Euphoria wrote:

>
> Thanks to all who posted. After trying all of the above-listed  
> options - the
> error is still popping up, but here is some progress:
>
> 1) I can read in the file just fine when I use the read.table  
> statement and
> specify it as a tab delimited file using the code:
>
> two <- read.table("Z:/CCFPhenotypesTAB.dat", head=TRUE, sep="\t")
>
> But, my issue is with GenABEL and the load.gwaa.data statement - I  
> need the
> file to be read into load.gwaa.data - unless there is another way to  
> read in
> the phenotype file in GenABEL.
>
> Code:
> mix <- load.gwaa.data (phe = "Z:/CCFPhenotypesTAB.dat", gen  =
> "pedmap-0.raw")

The first line of that function body is this:

dta <- read.table(phenofile, header = TRUE, as.is = TRUE)

Notice that no provision was made for a supplied sep argument. Hack it  
so that it recognizes tab characters. Just changing hte extension  
designation will not allter the fact that iwas not designed to work  
with "tab" as a separator.

Perhaps this as a replacement:

dta <- read.table(phenofile, header = TRUE, as.is = TRUE, sep="\t")

Or give the argument list a set of ellipses  , ...) and the above line  
some ellipses to receive the argument.


-- 
David.

>
>
> 2) Also, it might help if I explained how I came about the .dat  
> file.  It
> was originally created in excel as a .xlsx file, which I converted  
> to a tab
> delimited .txt file. I just changed the .txt extension to .dat for  
> it to be
> read in R for the GenABEL package.
>
> -- 
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>
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT