frq2R <- function( file ){
file <- file(file)
mylist <- strsplit(readLines(file), "\t")
close(file)
# create a list of mafs. If number of alleles != 2 then return NA.
maf.di.list <- lapply(mylist, function( line ) if( line[3]==2) line[6] else NA)
chr.di.list <- lapply(mylist, function( line ) if( line[3]==2) line[1] else NA)
pos.di.list <- lapply(mylist, function( line ) if( line[3]==2) line[2] else NA)
# convert to a numeric vector
maf.di <- as.numeric(unlist(maf.di.list))
chr.di <- as.factor(unlist(chr.di.list))
pos.di <- as.integer(unlist(pos.di.list))
# replace maf with 1 - maf for any maf > 0.5
maf.di <- ifelse( maf.di > 0.5, 1 - maf.di, maf.di )
return( data.frame( chr = chr.di, pos = pos.di, maf = maf.di ) )
}
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