| Detailed description |
When converting impute files to DatABEL format using impute2databel(), the screen output lists the wrong output file. For example:
impute2databel("HG19.for-impute.plink.chr1.ped.chunk1.impute2",
"HG19.for-impute.plink.chr1.ped.sample",
"HG19.for-impute.plink.chr1.ped.chunk1.genabel")
Options in effect:
--infile = HG19.for-impute.plink.chr1.ped.chunk1.impute2
--outfile = ./tmp64964
--skiprows = OFF
--skipcols = 5
--cnrow = OFF
--rncol = ON, using column 2 of 'HG19.for-impute.plink.chr1.ped.chunk1.impute2'
--transpose = ON
--Rmatrix = OFF
--nanString = NA
Here you see that outfile is listed as ./tmp64964 instead of the third argument of the function.
In line 36 of GenABEL's impute2databel() function a tmp file is created and this file is passed to the text2databel() function to be used for output. For the conversion this tmp file is used to create a temporary DatABEL object. Near the end of the impute2databel() function the temporary fv object is converted to a 'real' DatABEL file with the outfile name.
DatABEL's text2databel() function calls the function text2fvf_R() in DAlib, which, in turn, calls the C function text2fvf() in fvlib's convert_util.cpp. This function prints the options list unless the 'quiet' argument is true. Maybe we should set quiet to true when using impute2databel() in order to reduce confusion?
This behaviour is probably the same for other '2databel()' functions as well. |
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