Call the Mega2R functions to: create a .tped file, a .tfam file and a .phe file.
Then call the GenABEL functions to process these files: the .tped and the .tfam
file are processed by
convert.snp.tped to produce a tped.raw file. The latter
is combined with a .phe (phenotype) file by
load.gwaa.data to create a gwaa.data-class
object in memory. All these files are deleted when the exits.
data frame of markers to be processed
specify which map index to use for physical distances
'environment' containing SQLite database and other globals
gwaa.data-class object generated from the Mega2R database
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