[R] More info - S-Plus compatability

[Neil Shephard]

Dear all,

Thanks to those of you who have replied, the majority of the 
comments pointed out that the error caused by scan may originate 
from another function, and closer inspection of the output from 
traceback() reveals that it is in fact the read.table function where 
the error is originating from the full output of which I have included 
below.

The error msg I recieve is 

Error in scan(file = file, what = what, sep = sep, quote = quote, dec 
= dec, :
line 1 did not have 2 elements
Execution halted.

traceback()

8: scan(file=file, what=what, sep = sep, quote = quote, dec = dec, 
nmax = nrows, skip =0, na.strings, quiet = TRUE, fill = fill, 
strip.white = strip.white, nlak.lines.skip = blank.lines.skip, 
multi.line = FLASE, comment.char = comment.char)
7: read.table("_data\\TempFile, sep = ",", col.names = c("pair1", 
"pair2"))
6:ReadIBD.data("ibd.out")
5:RunGH(dat)
4:Read.Data(dat, x, HRallele)
3:eval.with.vis(expr, envir, enclos)
2:eval.with.vis(ei, envir)
1:source("TrendTest.Main.SSC")

grep -e 'read.table; *.SSC

indicates that the read.table() function is called in ReadIBD.SSC on 
lines seven and  twelve, and that the error is occuring with the 
second read.table() where the file '_Data\\TempFile' is being read 
(see copy of ReadIBD.data.SSC below).

ReadIBD.data_function(file) {
	
### Funtion to read the IBD probability data from GENEHUNTER 
### This data was generated from using "Dump IBD" command in 
GENEHUNTER
### File = ibd.out file from genehunter
	
	temp_read.table(file, skip=1, col.names=c("pos","pedid", "pair", 
		"prior.c0", "prior.c1", "prior.c2", "post.c0", "post.c1", 
"post.c2"), 
		row.names=NULL)

	write.table(temp$pair,file="_Data\\TempFile")		
	pairTemp_read.table("_Data\\TempFile", sep=",", 
col.names=c("pair1","pair2"))
	
	ibd_cbind.data.frame(temp,pairTemp)
	return(ibd)
}


Whilst not overly familiar with R/S-Plus syntax there are a couple 
of things I've noticed, firstly the second file that is trying to be read 
(where the error occurs) is actually called '_Data\TempFile' instead 
of '_Data\\TempFile'.  Secondly the columns do not appear to be 
seperated by "," as indicated in the read.table() statement, the 
numbers are encapsulated by "" and are seperated by blank space 
as shown in the sample below.

"x"
"1" "1,2"
"2" "1,3"
"3" "1,4"
..
..

I now have the problem of trying to workout why the "x" occurs on 
the first row (as this is clearly where the error is occuring as the 
Error statement indicates "line 1 did not have 2 elements").

grep -e '_Data' *.SSC

reveals that the _Data\\TempFile is created on the previous line of 
ReadIBD.Data.SSC after having read the file 'ibd.out'.  So I'm not 
sure why the first line is being created with "x" on the first line as 
the 'ibd.out' file is the correct format (I checked this visually).  It 
may be a problem with the way in which the 'ibd.out' file is being 
read by R that is causing this, but I'm not sure.

Can anyone see any potential problems with the read.table() and 
write.table() functions in the above script file???

Thanks again to all who offered help, and in anticipation of 
responses to this msg,

Regards

Neil

Neil Shephard
Genetics Statistician
ARC Epidemiology Unit, University of Manchester
neil.shephard at man.ac.uk
neil.shephard at mindless.com

"Contrariwise, if it was so, it might be; and if it
were so it would be; but as it isn't, it ain't. That's
logic" - Tweedledee (Alice Through the Looking Glass)