Description Usage Arguments Details
View source: R/plink-admixture-etc.R
This clearly does not preserve Ref and Alt alleles, etc., but can be a quick way to get to a bed file. It also allows the user to override the chromosome names so that they play nicely with ADMIXTURE. This function expects that plink is on the system PATH somewhere.
1 | convert_012_to_bed(W, chromo_override = FALSE, prefix = "plink")
|
W |
the matrix that results from |
chromo_override |
If TRUE, this sets the chromosome names to 1 so that ADMIXTURE will work. |
prefix |
Prefix for the output files. |
This function assumes everyone is unrelated and nobody has a phenotype to be coded in plink.
It also currently is hardwired to deal with contig names the way they come
out of our pipeline and get catenated by read_012
. That is,
when it sees: scaffold2|size4533513--4321992
it knows that the contig
comes before the – and the position in bp comes after that.
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