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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David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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